HEADER OXIDOREDUCTASE 25-SEP-15 5DYP
TITLE CRYSTAL STRUCTURE OF ASP251GLY/GLN307HIS MUTANT OF CYTOCHROME P450 BM3
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BIFUNCTIONAL P-450/NADPH-P450 REDUCTASE;
COMPND 3 CHAIN: A, C;
COMPND 4 SYNONYM: CYTOCHROME P450(BM-3),CYTOCHROME P450BM-3;
COMPND 5 EC: 1.14.14.1,1.6.2.4;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS MEGATERIUM;
SOURCE 3 ORGANISM_TAXID: 1404;
SOURCE 4 GENE: CYP102A1, CYP102;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS CYTOCHROME P450, RANDOM MUTAGENESIS, DRUG METABOLISM, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.DI NARDO,V.DELL'ANGELO,G.GILARDI
REVDAT 3 10-JAN-24 5DYP 1 REMARK
REVDAT 2 22-JUN-16 5DYP 1 JRNL
REVDAT 1 20-JAN-16 5DYP 0
JRNL AUTH G.DI NARDO,V.DELL'ANGELO,G.CATUCCI,S.J.SADEGHI,G.GILARDI
JRNL TITL SUBTLE STRUCTURAL CHANGES IN THE ASP251GLY/GLN307HIS P450
JRNL TITL 2 BM3 MUTANT RESPONSIBLE FOR NEW ACTIVITY TOWARD DICLOFENAC,
JRNL TITL 3 TOLBUTAMIDE AND IBUPROFEN.
JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 602 106 2016
JRNL REFN ESSN 1096-0384
JRNL PMID 26718083
JRNL DOI 10.1016/J.ABB.2015.12.005
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.00
REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 3 NUMBER OF REFLECTIONS : 41824
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.222
REMARK 3 R VALUE (WORKING SET) : 0.220
REMARK 3 FREE R VALUE : 0.257
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950
REMARK 3 FREE R VALUE TEST SET COUNT : 2071
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 47.0030 - 5.9153 0.95 2743 141 0.1801 0.2106
REMARK 3 2 5.9153 - 4.6966 0.97 2653 144 0.1880 0.1913
REMARK 3 3 4.6966 - 4.1033 0.97 2664 126 0.1707 0.2047
REMARK 3 4 4.1033 - 3.7283 0.97 2633 151 0.1899 0.2177
REMARK 3 5 3.7283 - 3.4611 0.98 2634 140 0.2193 0.2866
REMARK 3 6 3.4611 - 3.2571 0.99 2646 132 0.2423 0.2830
REMARK 3 7 3.2571 - 3.0941 0.99 2637 149 0.2572 0.3497
REMARK 3 8 3.0941 - 2.9594 0.99 2637 135 0.2705 0.2565
REMARK 3 9 2.9594 - 2.8455 0.99 2675 120 0.2780 0.3700
REMARK 3 10 2.8455 - 2.7473 0.99 2640 131 0.2791 0.3230
REMARK 3 11 2.7473 - 2.6614 0.99 2630 142 0.2917 0.3418
REMARK 3 12 2.6614 - 2.5853 0.99 2637 144 0.2977 0.3199
REMARK 3 13 2.5853 - 2.5173 0.99 2626 146 0.2977 0.3399
REMARK 3 14 2.5173 - 2.4559 1.00 2654 120 0.3066 0.4024
REMARK 3 15 2.4559 - 2.4000 0.99 2644 150 0.3123 0.3489
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.010
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 49.40
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.006 7443
REMARK 3 ANGLE : 1.228 10079
REMARK 3 CHIRALITY : 0.045 1078
REMARK 3 PLANARITY : 0.006 1301
REMARK 3 DIHEDRAL : 14.857 2797
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 7
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 52 )
REMARK 3 ORIGIN FOR THE GROUP (A): 1.4923 6.1506 3.2966
REMARK 3 T TENSOR
REMARK 3 T11: 0.6080 T22: 0.7687
REMARK 3 T33: 0.4452 T12: -0.1295
REMARK 3 T13: -0.1216 T23: 0.0428
REMARK 3 L TENSOR
REMARK 3 L11: 3.3653 L22: 5.5911
REMARK 3 L33: 0.7336 L12: 1.3401
REMARK 3 L13: -0.6855 L23: -0.8027
REMARK 3 S TENSOR
REMARK 3 S11: 0.1480 S12: -0.6654 S13: -0.1237
REMARK 3 S21: 0.3821 S22: 0.0977 S23: -0.2187
REMARK 3 S31: 0.5184 S32: 0.1975 S33: -0.1916
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 53 THROUGH 158 )
REMARK 3 ORIGIN FOR THE GROUP (A): 11.6421 20.3354 -19.0083
REMARK 3 T TENSOR
REMARK 3 T11: 0.2541 T22: 0.5294
REMARK 3 T33: 0.5839 T12: -0.1009
REMARK 3 T13: 0.0534 T23: -0.1767
REMARK 3 L TENSOR
REMARK 3 L11: 2.7458 L22: 1.5031
REMARK 3 L33: 5.1658 L12: -0.4848
REMARK 3 L13: 2.2242 L23: -0.0496
REMARK 3 S TENSOR
REMARK 3 S11: 0.4275 S12: 0.1943 S13: -0.1123
REMARK 3 S21: -0.0418 S22: 0.1034 S23: -0.5256
REMARK 3 S31: -0.1034 S32: 0.7267 S33: -0.3939
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 159 THROUGH 225 )
REMARK 3 ORIGIN FOR THE GROUP (A): 11.5105 7.9723 -28.8295
REMARK 3 T TENSOR
REMARK 3 T11: 1.2136 T22: 1.1947
REMARK 3 T33: 1.3079 T12: 0.0283
REMARK 3 T13: -0.3307 T23: -0.3510
REMARK 3 L TENSOR
REMARK 3 L11: 4.4655 L22: 0.7042
REMARK 3 L33: 6.1688 L12: -1.3555
REMARK 3 L13: 3.5252 L23: -0.2031
REMARK 3 S TENSOR
REMARK 3 S11: 1.4762 S12: -0.2244 S13: -1.6500
REMARK 3 S21: 0.0079 S22: 0.1549 S23: -0.5053
REMARK 3 S31: 2.6412 S32: 1.0403 S33: -1.0582
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 226 THROUGH 455 )
REMARK 3 ORIGIN FOR THE GROUP (A): 4.5871 24.9687 -15.1800
REMARK 3 T TENSOR
REMARK 3 T11: 0.2816 T22: 0.4874
REMARK 3 T33: 0.4670 T12: -0.0884
REMARK 3 T13: 0.1121 T23: -0.1933
REMARK 3 L TENSOR
REMARK 3 L11: 2.5905 L22: 1.9168
REMARK 3 L33: 4.4987 L12: 0.0774
REMARK 3 L13: 2.0140 L23: 0.2887
REMARK 3 S TENSOR
REMARK 3 S11: 0.2138 S12: -0.1041 S13: 0.2259
REMARK 3 S21: 0.0140 S22: 0.0657 S23: -0.2631
REMARK 3 S31: -0.3495 S32: 0.3028 S33: -0.2016
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 93 )
REMARK 3 ORIGIN FOR THE GROUP (A): -10.9798 0.0429 -76.2341
REMARK 3 T TENSOR
REMARK 3 T11: 0.8758 T22: 0.3757
REMARK 3 T33: 0.6713 T12: -0.1434
REMARK 3 T13: 0.2390 T23: -0.1128
REMARK 3 L TENSOR
REMARK 3 L11: 3.6406 L22: 1.5866
REMARK 3 L33: 5.1223 L12: 1.3780
REMARK 3 L13: 0.8094 L23: 1.7346
REMARK 3 S TENSOR
REMARK 3 S11: -0.3878 S12: 0.5183 S13: -0.8783
REMARK 3 S21: -0.8192 S22: 0.2912 S23: -0.4487
REMARK 3 S31: -0.2175 S32: 0.1712 S33: 0.1089
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 94 THROUGH 311 )
REMARK 3 ORIGIN FOR THE GROUP (A): -8.6212 17.2622 -55.6097
REMARK 3 T TENSOR
REMARK 3 T11: 0.7792 T22: 0.3389
REMARK 3 T33: 0.4270 T12: 0.0201
REMARK 3 T13: 0.0839 T23: 0.0210
REMARK 3 L TENSOR
REMARK 3 L11: 5.9224 L22: 2.2621
REMARK 3 L33: 5.4020 L12: 1.2180
REMARK 3 L13: 1.8326 L23: 1.9630
REMARK 3 S TENSOR
REMARK 3 S11: -0.0962 S12: -0.2078 S13: -0.2828
REMARK 3 S21: -0.7008 S22: 0.1006 S23: 0.1155
REMARK 3 S31: -0.8551 S32: -0.1511 S33: -0.0793
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 312 THROUGH 456 )
REMARK 3 ORIGIN FOR THE GROUP (A): 0.3347 14.3927 -70.7694
REMARK 3 T TENSOR
REMARK 3 T11: 1.0358 T22: 0.6392
REMARK 3 T33: 0.5233 T12: -0.3652
REMARK 3 T13: 0.3062 T23: -0.0537
REMARK 3 L TENSOR
REMARK 3 L11: 1.9301 L22: 2.2181
REMARK 3 L33: 3.7910 L12: 0.5529
REMARK 3 L13: 0.9659 L23: 1.9000
REMARK 3 S TENSOR
REMARK 3 S11: -0.4183 S12: 0.3647 S13: -0.1812
REMARK 3 S21: -0.8653 S22: 0.5925 S23: -0.4668
REMARK 3 S31: -1.2163 S32: 0.8475 S33: -0.1082
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5DYP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-15.
REMARK 100 THE DEPOSITION ID IS D_1000213554.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-MAR-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALBA
REMARK 200 BEAMLINE : XALOC
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41881
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 48.980
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6
REMARK 200 DATA REDUNDANCY : 5.500
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 5.50
REMARK 200 R MERGE FOR SHELL (I) : 0.51700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 1JPZ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 100 MM CACODYLIC ACID PH
REMARK 280 5.5-6.8, 100-160 MM MGCL2, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.56700
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.47350
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.22400
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.47350
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.56700
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.22400
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4470 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 36690 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 THR A 1
REMARK 465 GLN A 189
REMARK 465 ARG A 190
REMARK 465 ALA A 191
REMARK 465 ASN A 192
REMARK 465 PRO A 193
REMARK 465 ASP A 194
REMARK 465 ASP A 195
REMARK 465 PRO A 196
REMARK 465 ALA A 197
REMARK 465 TYR A 198
REMARK 465 ASP A 199
REMARK 465 GLU A 200
REMARK 465 GLY A 227
REMARK 465 GLU A 228
REMARK 465 GLY A 456
REMARK 465 GLY A 457
REMARK 465 ILE A 458
REMARK 465 PRO A 459
REMARK 465 SER A 460
REMARK 465 PRO A 461
REMARK 465 SER A 462
REMARK 465 THR A 463
REMARK 465 GLU A 464
REMARK 465 GLN A 465
REMARK 465 SER A 466
REMARK 465 ALA A 467
REMARK 465 LYS A 468
REMARK 465 LYS A 469
REMARK 465 VAL A 470
REMARK 465 ARG C 190
REMARK 465 ALA C 191
REMARK 465 ASN C 192
REMARK 465 PRO C 193
REMARK 465 GLY C 227
REMARK 465 GLU C 228
REMARK 465 GLY C 457
REMARK 465 ILE C 458
REMARK 465 PRO C 459
REMARK 465 SER C 460
REMARK 465 PRO C 461
REMARK 465 SER C 462
REMARK 465 THR C 463
REMARK 465 GLU C 464
REMARK 465 GLN C 465
REMARK 465 SER C 466
REMARK 465 ALA C 467
REMARK 465 LYS C 468
REMARK 465 LYS C 469
REMARK 465 VAL C 470
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O LYS A 113 O HOH A 601 1.81
REMARK 500 O ASP C 84 O HOH C 601 1.81
REMARK 500 OE1 GLN A 125 O HOH A 602 1.87
REMARK 500 O ILE A 401 O HOH A 603 1.90
REMARK 500 O HOH A 689 O HOH A 692 1.95
REMARK 500 O LYS C 349 O HOH C 602 1.96
REMARK 500 O ILE C 219 O HOH C 603 2.10
REMARK 500 OE2 GLU C 348 O HOH C 604 2.10
REMARK 500 NZ LYS C 440 O HOH C 605 2.11
REMARK 500 OD2 ASP C 84 O HOH C 606 2.12
REMARK 500 O HOH A 683 O HOH A 694 2.13
REMARK 500 O ALA C 389 O HOH C 607 2.15
REMARK 500 O HOH A 681 O HOH A 697 2.15
REMARK 500 O HOH A 687 O HOH A 694 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 LYS A 210 CA - CB - CG ANGL. DEV. = 13.4 DEGREES
REMARK 500 PRO C 243 C - N - CA ANGL. DEV. = -13.9 DEGREES
REMARK 500 PRO C 376 C - N - CA ANGL. DEV. = 9.3 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 PHE A 11 69.27 -118.17
REMARK 500 LYS A 15 -125.23 53.80
REMARK 500 ASP A 84 41.54 -99.10
REMARK 500 LYS A 202 -123.44 -32.65
REMARK 500 ASP A 232 -164.25 -116.80
REMARK 500 HIS A 266 -43.92 -151.32
REMARK 500 GLU A 344 -41.17 -134.72
REMARK 500 LEU A 437 -24.78 67.60
REMARK 500 PHE C 11 67.72 -110.61
REMARK 500 LYS C 15 -124.57 56.57
REMARK 500 PRO C 18 -8.42 -59.91
REMARK 500 ASP C 84 40.93 -99.68
REMARK 500 ASP C 232 -162.80 -120.66
REMARK 500 PRO C 243 30.73 -89.76
REMARK 500 HIS C 266 -42.40 -152.81
REMARK 500 GLU C 344 -39.85 -134.77
REMARK 500 ASP C 370 57.60 -90.86
REMARK 500 THR C 436 59.76 -148.08
REMARK 500 LEU C 437 -22.86 66.00
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 HEM A 501 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 400 SG
REMARK 620 2 HEM A 501 NA 102.7
REMARK 620 3 HEM A 501 NB 88.2 89.6
REMARK 620 4 HEM A 501 NC 85.9 171.2 89.2
REMARK 620 5 HEM A 501 ND 100.2 89.4 171.5 90.5
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 HEM C 501 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS C 400 SG
REMARK 620 2 HEM C 501 NA 100.6
REMARK 620 3 HEM C 501 NB 91.4 89.0
REMARK 620 4 HEM C 501 NC 83.0 176.3 89.9
REMARK 620 5 HEM C 501 ND 91.0 89.3 177.2 91.7
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue HEM C 501
DBREF 5DYP A 1 470 UNP P14779 CPXB_BACME 2 471
DBREF 5DYP C 1 470 UNP P14779 CPXB_BACME 2 471
SEQADV 5DYP GLY A 251 UNP P14779 ASP 252 ENGINEERED MUTATION
SEQADV 5DYP HIS A 307 UNP P14779 GLN 308 ENGINEERED MUTATION
SEQADV 5DYP GLY C 251 UNP P14779 ASP 252 ENGINEERED MUTATION
SEQADV 5DYP HIS C 307 UNP P14779 GLN 308 ENGINEERED MUTATION
SEQRES 1 A 470 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU
SEQRES 2 A 470 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL
SEQRES 3 A 470 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE
SEQRES 4 A 470 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU
SEQRES 5 A 470 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER
SEQRES 6 A 470 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL
SEQRES 7 A 470 ARG ASP PHE ALA GLY ASP GLY LEU PHE THR SER TRP THR
SEQRES 8 A 470 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU
SEQRES 9 A 470 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA
SEQRES 10 A 470 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP
SEQRES 11 A 470 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU
SEQRES 12 A 470 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS
SEQRES 13 A 470 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN
SEQRES 14 A 470 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP
SEQRES 15 A 470 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP
SEQRES 16 A 470 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP
SEQRES 17 A 470 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA
SEQRES 18 A 470 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU
SEQRES 19 A 470 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU
SEQRES 20 A 470 PRO LEU ASP GLY GLU ASN ILE ARG TYR GLN ILE ILE THR
SEQRES 21 A 470 PHE LEU ILE ALA GLY HIS GLU THR THR SER GLY LEU LEU
SEQRES 22 A 470 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL
SEQRES 23 A 470 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL
SEQRES 24 A 470 ASP PRO VAL PRO SER TYR LYS HIS VAL LYS GLN LEU LYS
SEQRES 25 A 470 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP
SEQRES 26 A 470 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP
SEQRES 27 A 470 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP
SEQRES 28 A 470 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS
SEQRES 29 A 470 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU
SEQRES 30 A 470 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE
SEQRES 31 A 470 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN
SEQRES 32 A 470 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET
SEQRES 33 A 470 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR
SEQRES 34 A 470 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU
SEQRES 35 A 470 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU
SEQRES 36 A 470 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS
SEQRES 37 A 470 LYS VAL
SEQRES 1 C 470 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU
SEQRES 2 C 470 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL
SEQRES 3 C 470 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE
SEQRES 4 C 470 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU
SEQRES 5 C 470 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER
SEQRES 6 C 470 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL
SEQRES 7 C 470 ARG ASP PHE ALA GLY ASP GLY LEU PHE THR SER TRP THR
SEQRES 8 C 470 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU
SEQRES 9 C 470 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA
SEQRES 10 C 470 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP
SEQRES 11 C 470 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU
SEQRES 12 C 470 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS
SEQRES 13 C 470 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN
SEQRES 14 C 470 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP
SEQRES 15 C 470 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP
SEQRES 16 C 470 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP
SEQRES 17 C 470 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA
SEQRES 18 C 470 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU
SEQRES 19 C 470 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU
SEQRES 20 C 470 PRO LEU ASP GLY GLU ASN ILE ARG TYR GLN ILE ILE THR
SEQRES 21 C 470 PHE LEU ILE ALA GLY HIS GLU THR THR SER GLY LEU LEU
SEQRES 22 C 470 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL
SEQRES 23 C 470 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL
SEQRES 24 C 470 ASP PRO VAL PRO SER TYR LYS HIS VAL LYS GLN LEU LYS
SEQRES 25 C 470 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP
SEQRES 26 C 470 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP
SEQRES 27 C 470 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP
SEQRES 28 C 470 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS
SEQRES 29 C 470 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU
SEQRES 30 C 470 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE
SEQRES 31 C 470 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN
SEQRES 32 C 470 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET
SEQRES 33 C 470 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR
SEQRES 34 C 470 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU
SEQRES 35 C 470 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU
SEQRES 36 C 470 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS
SEQRES 37 C 470 LYS VAL
HET HEM A 501 43
HET HEM C 501 43
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETSYN HEM HEME
FORMUL 3 HEM 2(C34 H32 FE N4 O4)
FORMUL 5 HOH *148(H2 O)
HELIX 1 AA1 PHE A 11 LYS A 15 5 5
HELIX 2 AA2 ASN A 16 ASN A 21 5 6
HELIX 3 AA3 LYS A 24 GLY A 37 1 14
HELIX 4 AA4 SER A 54 CYS A 62 1 9
HELIX 5 AA5 SER A 72 GLY A 83 1 12
HELIX 6 AA6 GLU A 93 LEU A 104 1 12
HELIX 7 AA7 PRO A 105 PHE A 107 5 3
HELIX 8 AA8 SER A 108 LYS A 113 1 6
HELIX 9 AA9 TYR A 115 ARG A 132 1 18
HELIX 10 AB1 VAL A 141 ASN A 159 1 19
HELIX 11 AB2 ASN A 163 ARG A 167 5 5
HELIX 12 AB3 HIS A 171 LYS A 187 1 17
HELIX 13 AB4 GLN A 204 SER A 226 1 23
HELIX 14 AB5 ASP A 232 GLY A 240 1 9
HELIX 15 AB6 ASP A 250 GLY A 265 1 16
HELIX 16 AB7 HIS A 266 ASN A 283 1 18
HELIX 17 AB8 ASN A 283 LEU A 298 1 16
HELIX 18 AB9 SER A 304 LYS A 309 1 6
HELIX 19 AC1 LEU A 311 TRP A 325 1 15
HELIX 20 AC2 ILE A 357 HIS A 361 1 5
HELIX 21 AC3 ASP A 363 GLY A 368 1 6
HELIX 22 AC4 ARG A 375 GLU A 380 5 6
HELIX 23 AC5 ASN A 395 ALA A 399 5 5
HELIX 24 AC6 GLY A 402 HIS A 420 1 19
HELIX 25 AC7 PHE C 11 LYS C 15 5 5
HELIX 26 AC8 ASN C 16 ASN C 21 5 6
HELIX 27 AC9 LYS C 24 GLY C 37 1 14
HELIX 28 AD1 SER C 54 CYS C 62 1 9
HELIX 29 AD2 SER C 72 GLY C 83 1 12
HELIX 30 AD3 GLU C 93 LEU C 104 1 12
HELIX 31 AD4 PRO C 105 SER C 108 5 4
HELIX 32 AD5 ALA C 111 ARG C 132 1 22
HELIX 33 AD6 VAL C 141 ASN C 159 1 19
HELIX 34 AD7 ASN C 163 ARG C 167 5 5
HELIX 35 AD8 HIS C 171 LEU C 188 1 18
HELIX 36 AD9 PRO C 196 SER C 226 1 31
HELIX 37 AE1 ASP C 232 GLY C 240 1 9
HELIX 38 AE2 ASP C 250 GLY C 265 1 16
HELIX 39 AE3 HIS C 266 ASN C 283 1 18
HELIX 40 AE4 ASN C 283 LEU C 298 1 16
HELIX 41 AE5 SER C 304 LYS C 309 1 6
HELIX 42 AE6 LEU C 311 TRP C 325 1 15
HELIX 43 AE7 ILE C 357 HIS C 361 1 5
HELIX 44 AE8 ASP C 363 GLY C 368 1 6
HELIX 45 AE9 ARG C 375 GLU C 380 5 6
HELIX 46 AF1 ASN C 395 ALA C 399 5 5
HELIX 47 AF2 GLY C 402 HIS C 420 1 19
SHEET 1 AA1 5 ILE A 39 ALA A 44 0
SHEET 2 AA1 5 ARG A 47 LEU A 52 -1 O THR A 49 N PHE A 42
SHEET 3 AA1 5 GLU A 352 LEU A 356 1 O MET A 354 N LEU A 52
SHEET 4 AA1 5 ALA A 330 ALA A 335 -1 N PHE A 331 O VAL A 355
SHEET 5 AA1 5 PHE A 67 LYS A 69 -1 N ASP A 68 O TYR A 334
SHEET 1 AA2 3 ILE A 139 GLU A 140 0
SHEET 2 AA2 3 VAL A 445 SER A 450 -1 O VAL A 446 N ILE A 139
SHEET 3 AA2 3 PHE A 421 GLU A 424 -1 N ASP A 422 O LYS A 449
SHEET 1 AA3 2 THR A 339 LEU A 341 0
SHEET 2 AA3 2 TYR A 345 LEU A 347 -1 O LEU A 347 N THR A 339
SHEET 1 AA4 2 ILE A 433 GLU A 435 0
SHEET 2 AA4 2 LEU A 439 PRO A 441 -1 O LYS A 440 N LYS A 434
SHEET 1 AA5 5 ILE C 39 ALA C 44 0
SHEET 2 AA5 5 ARG C 47 LEU C 52 -1 O THR C 49 N PHE C 42
SHEET 3 AA5 5 GLU C 352 LEU C 356 1 O MET C 354 N ARG C 50
SHEET 4 AA5 5 ALA C 330 ALA C 335 -1 N PHE C 331 O VAL C 355
SHEET 5 AA5 5 PHE C 67 LYS C 69 -1 N ASP C 68 O TYR C 334
SHEET 1 AA6 3 ILE C 139 GLU C 140 0
SHEET 2 AA6 3 VAL C 445 SER C 450 -1 O VAL C 446 N ILE C 139
SHEET 3 AA6 3 PHE C 421 GLU C 424 -1 N GLU C 424 O LYS C 447
SHEET 1 AA7 2 THR C 339 LEU C 341 0
SHEET 2 AA7 2 TYR C 345 LEU C 347 -1 O LEU C 347 N THR C 339
SHEET 1 AA8 2 ILE C 433 GLU C 435 0
SHEET 2 AA8 2 LEU C 439 PRO C 441 -1 O LYS C 440 N LYS C 434
LINK SG CYS A 400 FE HEM A 501 1555 1555 2.30
LINK SG CYS C 400 FE HEM C 501 1555 1555 2.30
SITE 1 AC1 25 LYS A 69 LEU A 86 PHE A 87 TRP A 96
SITE 2 AC1 25 ILE A 153 ALA A 264 GLY A 265 THR A 268
SITE 3 AC1 25 THR A 269 THR A 327 ALA A 328 PHE A 331
SITE 4 AC1 25 PRO A 392 PHE A 393 GLY A 394 ARG A 398
SITE 5 AC1 25 ALA A 399 CYS A 400 ILE A 401 GLY A 402
SITE 6 AC1 25 ALA A 406 HOH A 616 HOH A 635 HOH A 637
SITE 7 AC1 25 HOH A 670
SITE 1 AC2 24 LYS C 69 LEU C 86 PHE C 87 TRP C 96
SITE 2 AC2 24 ALA C 264 GLY C 265 THR C 268 THR C 269
SITE 3 AC2 24 LEU C 272 THR C 327 ALA C 328 PHE C 331
SITE 4 AC2 24 PRO C 392 PHE C 393 GLY C 394 ARG C 398
SITE 5 AC2 24 CYS C 400 ILE C 401 GLY C 402 ALA C 406
SITE 6 AC2 24 HOH C 613 HOH C 616 HOH C 620 HOH C 640
CRYST1 61.134 118.448 146.947 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.016358 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008443 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006805 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
