HEADER OXIDOREDUCTASE 14-SEP-16 5TC4
TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL METHYLENETETRAHYDROFOLATE
TITLE 2 DEHYDROGENASE-CYCLOHYDROLASE (MTHFD2) IN COMPLEX WITH LY345899 AND
TITLE 3 COFACTORS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BIFUNCTIONAL METHYLENETETRAHYDROFOLATE
COMPND 3 DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL;
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: UNP RESIDUES 36-350;
COMPND 6 EC: 1.5.1.15,3.5.4.9;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: MTHFD2, NMDMC;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008
KEYWDS INHIBITOR, FOLATE, COFACTOR, DEHYDROGENASE, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.GUSTAFSSON,A.-S.JEMTH,N.GUSTAFSSON SHEPPARD,K.FARNEGARDH,O.LOSEVA,
AUTHOR 2 E.WIITA,N.BONAGAS,L.DAHLLUND,S.LLONA-MINGUEZ,M.HAGGBLAD,
AUTHOR 3 M.HENRIKSSON,Y.ANDERSSON,E.HOMAN,T.HELLEDAY,P.STENMARK
REVDAT 5 17-JAN-24 5TC4 1 COMPND HETNAM
REVDAT 4 13-SEP-17 5TC4 1 REMARK
REVDAT 3 16-AUG-17 5TC4 1 REMARK
REVDAT 2 01-MAR-17 5TC4 1 JRNL
REVDAT 1 14-DEC-16 5TC4 0
JRNL AUTH R.GUSTAFSSON,A.S.JEMTH,N.M.GUSTAFSSON,K.FARNEGARDH,O.LOSEVA,
JRNL AUTH 2 E.WIITA,N.BONAGAS,L.DAHLLUND,S.LLONA-MINGUEZ,M.HAGGBLAD,
JRNL AUTH 3 M.HENRIKSSON,Y.ANDERSSON,E.HOMAN,T.HELLEDAY,P.STENMARK
JRNL TITL CRYSTAL STRUCTURE OF THE EMERGING CANCER TARGET MTHFD2 IN
JRNL TITL 2 COMPLEX WITH A SUBSTRATE-BASED INHIBITOR.
JRNL REF CANCER RES. V. 77 937 2017
JRNL REFN ESSN 1538-7445
JRNL PMID 27899380
JRNL DOI 10.1158/0008-5472.CAN-16-1476
REMARK 2
REMARK 2 RESOLUTION. 1.89 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.16
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 20245
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.165
REMARK 3 R VALUE (WORKING SET) : 0.163
REMARK 3 FREE R VALUE : 0.212
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1073
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.89
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1463
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40
REMARK 3 BIN R VALUE (WORKING SET) : 0.3480
REMARK 3 BIN FREE R VALUE SET COUNT : 71
REMARK 3 BIN FREE R VALUE : 0.3050
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2216
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 83
REMARK 3 SOLVENT ATOMS : 214
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.27
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.04000
REMARK 3 B22 (A**2) : 0.04000
REMARK 3 B33 (A**2) : -0.08000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.158
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.818
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2379 ; 0.023 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 2346 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3244 ; 2.276 ; 2.006
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5401 ; 1.170 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 6.042 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;42.827 ;24.778
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 410 ;15.236 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.267 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.137 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2646 ; 0.011 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 497 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1184 ; 0.901 ; 1.295
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1184 ; 0.897 ; 1.295
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1480 ; 1.430 ; 1.927
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1481 ; 1.431 ; 1.930
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1195 ; 1.642 ; 1.663
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1192 ; 1.640 ; 1.663
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1759 ; 2.602 ; 2.412
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2789 ; 6.253 ;12.452
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2715 ; 6.066 ;11.835
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 7
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 36 A 59
REMARK 3 ORIGIN FOR THE GROUP (A): 84.4053 9.5968 -2.9965
REMARK 3 T TENSOR
REMARK 3 T11: 0.0726 T22: 0.2043
REMARK 3 T33: 0.2370 T12: -0.0230
REMARK 3 T13: -0.0114 T23: -0.0814
REMARK 3 L TENSOR
REMARK 3 L11: 1.9396 L22: 1.2393
REMARK 3 L33: 20.9785 L12: 1.0531
REMARK 3 L13: -5.9999 L23: -3.5590
REMARK 3 S TENSOR
REMARK 3 S11: -0.0955 S12: 0.3022 S13: 0.0086
REMARK 3 S21: -0.0205 S22: -0.1128 S23: 0.2910
REMARK 3 S31: 0.1668 S32: -0.8843 S33: 0.2083
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 60 A 142
REMARK 3 ORIGIN FOR THE GROUP (A): 99.1696 17.9708 14.3693
REMARK 3 T TENSOR
REMARK 3 T11: 0.1952 T22: 0.1584
REMARK 3 T33: 0.0436 T12: 0.0362
REMARK 3 T13: 0.0265 T23: -0.0020
REMARK 3 L TENSOR
REMARK 3 L11: 0.5046 L22: 1.1266
REMARK 3 L33: 0.2349 L12: 0.4644
REMARK 3 L13: 0.2387 L23: 0.2556
REMARK 3 S TENSOR
REMARK 3 S11: -0.0815 S12: -0.0363 S13: 0.1079
REMARK 3 S21: 0.1764 S22: 0.0059 S23: 0.1258
REMARK 3 S31: -0.0367 S32: 0.0032 S33: 0.0757
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 143 A 185
REMARK 3 ORIGIN FOR THE GROUP (A): 102.3112 4.1313 5.7143
REMARK 3 T TENSOR
REMARK 3 T11: 0.1881 T22: 0.1583
REMARK 3 T33: 0.0419 T12: -0.0019
REMARK 3 T13: 0.0208 T23: -0.0004
REMARK 3 L TENSOR
REMARK 3 L11: 0.0305 L22: 0.3582
REMARK 3 L33: 1.2147 L12: 0.0736
REMARK 3 L13: 0.0037 L23: 0.4351
REMARK 3 S TENSOR
REMARK 3 S11: -0.0027 S12: -0.0094 S13: 0.0311
REMARK 3 S21: 0.0935 S22: -0.0449 S23: 0.0977
REMARK 3 S31: 0.0599 S32: -0.0037 S33: 0.0476
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 186 A 275
REMARK 3 ORIGIN FOR THE GROUP (A): 105.0876 4.8474 -12.7991
REMARK 3 T TENSOR
REMARK 3 T11: 0.1703 T22: 0.1630
REMARK 3 T33: 0.0204 T12: 0.0047
REMARK 3 T13: -0.0111 T23: 0.0080
REMARK 3 L TENSOR
REMARK 3 L11: 0.6548 L22: 0.6972
REMARK 3 L33: 0.4834 L12: 0.0098
REMARK 3 L13: -0.1159 L23: -0.1043
REMARK 3 S TENSOR
REMARK 3 S11: 0.0184 S12: 0.0796 S13: 0.0056
REMARK 3 S21: 0.0062 S22: -0.0029 S23: 0.0631
REMARK 3 S31: -0.0014 S32: -0.0026 S33: -0.0154
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 276 A 289
REMARK 3 ORIGIN FOR THE GROUP (A): 101.3750 28.4525 -10.3762
REMARK 3 T TENSOR
REMARK 3 T11: 0.3838 T22: 0.1374
REMARK 3 T33: 0.5440 T12: 0.1689
REMARK 3 T13: 0.1662 T23: -0.0548
REMARK 3 L TENSOR
REMARK 3 L11: 3.6544 L22: 33.9544
REMARK 3 L33: 4.7511 L12: -9.2438
REMARK 3 L13: 2.6314 L23: -1.1798
REMARK 3 S TENSOR
REMARK 3 S11: -0.6429 S12: -0.4810 S13: 0.4208
REMARK 3 S21: 0.6170 S22: 0.3327 S23: -1.1395
REMARK 3 S31: -0.9317 S32: -0.8034 S33: 0.3103
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 290 A 320
REMARK 3 ORIGIN FOR THE GROUP (A): 95.0852 14.6726 -13.7554
REMARK 3 T TENSOR
REMARK 3 T11: 0.1198 T22: 0.1032
REMARK 3 T33: 0.2906 T12: 0.0415
REMARK 3 T13: -0.0617 T23: 0.0016
REMARK 3 L TENSOR
REMARK 3 L11: 1.1838 L22: 0.4256
REMARK 3 L33: 3.8727 L12: -0.2800
REMARK 3 L13: -1.0008 L23: 0.2205
REMARK 3 S TENSOR
REMARK 3 S11: 0.0774 S12: 0.0929 S13: 0.2825
REMARK 3 S21: -0.1298 S22: -0.0751 S23: 0.2008
REMARK 3 S31: 0.0423 S32: -0.0237 S33: -0.0023
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 321 A 332
REMARK 3 ORIGIN FOR THE GROUP (A): 92.3162 3.7785 12.0475
REMARK 3 T TENSOR
REMARK 3 T11: 0.1655 T22: 0.1476
REMARK 3 T33: 0.1654 T12: -0.0085
REMARK 3 T13: 0.0396 T23: -0.0172
REMARK 3 L TENSOR
REMARK 3 L11: 1.2974 L22: 5.2598
REMARK 3 L33: 9.4520 L12: 1.3564
REMARK 3 L13: -1.7021 L23: -2.0232
REMARK 3 S TENSOR
REMARK 3 S11: -0.0191 S12: -0.1073 S13: -0.2726
REMARK 3 S21: -0.0232 S22: -0.0022 S23: 0.1225
REMARK 3 S31: 0.6935 S32: 0.1980 S33: 0.0213
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5TC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-16.
REMARK 100 THE DEPOSITION ID IS D_1000223716.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-SEP-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : MASSIF-3
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21322
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890
REMARK 200 RESOLUTION RANGE LOW (A) : 37.160
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 6.900
REMARK 200 R MERGE (I) : 0.31600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8
REMARK 200 DATA REDUNDANCY IN SHELL : 6.70
REMARK 200 R MERGE FOR SHELL (I) : 4.34800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 1B0A
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.02
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE/CITRATE PH 4.1, 38 %
REMARK 280 V/V PEG300, IN PRESENCE OF 1:50 RATIO EACH OF TRYPSIN, ALPHA-
REMARK 280 CHYMOTRYPSIN, PEPSIN, PAPAIN, PROTEINASE K AND SUBTILISIN TO
REMARK 280 MTHFD2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -Y,X,Z
REMARK 290 4555 Y,-X,Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2
REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.16150
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.16150
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.31000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.16150
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.16150
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.31000
REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 37.16150
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 37.16150
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 49.31000
REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 37.16150
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 37.16150
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 49.31000
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: 6150 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 23020 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 350 BIOMT1 2 -1.000000 0.000000 0.000000 222.96900
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 599 LIES ON A SPECIAL POSITION.
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 MET A 35
REMARK 465 ASP A 281
REMARK 465 PRO A 282
REMARK 465 VAL A 283
REMARK 465 THR A 284
REMARK 465 ALA A 285
REMARK 465 ARG A 333
REMARK 465 LEU A 334
REMARK 465 GLU A 335
REMARK 465 GLU A 336
REMARK 465 ARG A 337
REMARK 465 GLU A 338
REMARK 465 VAL A 339
REMARK 465 LEU A 340
REMARK 465 LYS A 341
REMARK 465 SER A 342
REMARK 465 LYS A 343
REMARK 465 GLU A 344
REMARK 465 LEU A 345
REMARK 465 GLY A 346
REMARK 465 VAL A 347
REMARK 465 ALA A 348
REMARK 465 THR A 349
REMARK 465 ASN A 350
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 TYR A 170 CE1 TYR A 170 CZ 0.095
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 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 ASP A 123 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ASP A 124 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 LYS A 185 CD - CE - NZ ANGL. DEV. = 14.3 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 VAL A 205 -73.02 -128.84
REMARK 500 HIS A 232 -164.87 -162.13
REMARK 500 ALA A 253 55.04 -140.38
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 711 DISTANCE = 5.83 ANGSTROMS
REMARK 525 HOH A 712 DISTANCE = 7.14 ANGSTROMS
REMARK 525 HOH A 713 DISTANCE = 7.31 ANGSTROMS
REMARK 525 HOH A 714 DISTANCE = 12.68 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue L34 A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 403
DBREF 5TC4 A 36 350 UNP P13995 MTDC_HUMAN 36 350
SEQADV 5TC4 MET A 35 UNP P13995 INITIATING METHIONINE
SEQRES 1 A 316 MET GLU ALA VAL VAL ILE SER GLY ARG LYS LEU ALA GLN
SEQRES 2 A 316 GLN ILE LYS GLN GLU VAL ARG GLN GLU VAL GLU GLU TRP
SEQRES 3 A 316 VAL ALA SER GLY ASN LYS ARG PRO HIS LEU SER VAL ILE
SEQRES 4 A 316 LEU VAL GLY GLU ASN PRO ALA SER HIS SER TYR VAL LEU
SEQRES 5 A 316 ASN LYS THR ARG ALA ALA ALA VAL VAL GLY ILE ASN SER
SEQRES 6 A 316 GLU THR ILE MET LYS PRO ALA SER ILE SER GLU GLU GLU
SEQRES 7 A 316 LEU LEU ASN LEU ILE ASN LYS LEU ASN ASN ASP ASP ASN
SEQRES 8 A 316 VAL ASP GLY LEU LEU VAL GLN LEU PRO LEU PRO GLU HIS
SEQRES 9 A 316 ILE ASP GLU ARG ARG ILE CYS ASN ALA VAL SER PRO ASP
SEQRES 10 A 316 LYS ASP VAL ASP GLY PHE HIS VAL ILE ASN VAL GLY ARG
SEQRES 11 A 316 MET CYS LEU ASP GLN TYR SER MET LEU PRO ALA THR PRO
SEQRES 12 A 316 TRP GLY VAL TRP GLU ILE ILE LYS ARG THR GLY ILE PRO
SEQRES 13 A 316 THR LEU GLY LYS ASN VAL VAL VAL ALA GLY ARG SER LYS
SEQRES 14 A 316 ASN VAL GLY MET PRO ILE ALA MET LEU LEU HIS THR ASP
SEQRES 15 A 316 GLY ALA HIS GLU ARG PRO GLY GLY ASP ALA THR VAL THR
SEQRES 16 A 316 ILE SER HIS ARG TYR THR PRO LYS GLU GLN LEU LYS LYS
SEQRES 17 A 316 HIS THR ILE LEU ALA ASP ILE VAL ILE SER ALA ALA GLY
SEQRES 18 A 316 ILE PRO ASN LEU ILE THR ALA ASP MET ILE LYS GLU GLY
SEQRES 19 A 316 ALA ALA VAL ILE ASP VAL GLY ILE ASN ARG VAL HIS ASP
SEQRES 20 A 316 PRO VAL THR ALA LYS PRO LYS LEU VAL GLY ASP VAL ASP
SEQRES 21 A 316 PHE GLU GLY VAL ARG GLN LYS ALA GLY TYR ILE THR PRO
SEQRES 22 A 316 VAL PRO GLY GLY VAL GLY PRO MET THR VAL ALA MET LEU
SEQRES 23 A 316 MET LYS ASN THR ILE ILE ALA ALA LYS LYS VAL LEU ARG
SEQRES 24 A 316 LEU GLU GLU ARG GLU VAL LEU LYS SER LYS GLU LEU GLY
SEQRES 25 A 316 VAL ALA THR ASN
HET NAD A 401 44
HET L34 A 402 34
HET PO4 A 403 5
HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM L34 4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,
HETNAM 2 L34 9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-
HETNAM 3 L34 PHENYLCARBONYL-GLUTAMI C ACID
HETNAM PO4 PHOSPHATE ION
HETSYN L34 LY345899
FORMUL 2 NAD C21 H27 N7 O14 P2
FORMUL 3 L34 C20 H21 N7 O7
FORMUL 4 PO4 O4 P 3-
FORMUL 5 HOH *214(H2 O)
HELIX 1 AA1 SER A 41 SER A 63 1 23
HELIX 2 AA2 ASN A 78 GLY A 96 1 19
HELIX 3 AA3 SER A 109 ASP A 123 1 15
HELIX 4 AA4 ASP A 140 VAL A 148 1 9
HELIX 5 AA5 SER A 149 ASP A 153 5 5
HELIX 6 AA6 HIS A 158 LEU A 167 1 10
HELIX 7 AA7 PRO A 174 GLY A 188 1 15
HELIX 8 AA8 VAL A 205 THR A 215 1 11
HELIX 9 AA9 PRO A 236 ILE A 245 1 10
HELIX 10 AB1 THR A 261 ILE A 265 5 5
HELIX 11 AB2 ASP A 294 ARG A 299 1 6
HELIX 12 AB3 GLY A 311 LYS A 330 1 20
SHEET 1 AA1 6 VAL A 38 VAL A 39 0
SHEET 2 AA1 6 TYR A 304 ILE A 305 1 O ILE A 305 N VAL A 38
SHEET 3 AA1 6 ALA A 270 ASP A 273 1 N VAL A 271 O TYR A 304
SHEET 4 AA1 6 ILE A 249 SER A 252 1 N VAL A 250 O ALA A 270
SHEET 5 AA1 6 ASN A 195 ALA A 199 1 N VAL A 197 O ILE A 251
SHEET 6 AA1 6 THR A 227 SER A 231 1 O THR A 227 N VAL A 196
SHEET 1 AA2 3 ASN A 98 LYS A 104 0
SHEET 2 AA2 3 HIS A 69 VAL A 75 1 N VAL A 72 O GLU A 100
SHEET 3 AA2 3 GLY A 128 VAL A 131 1 O GLY A 128 N SER A 71
SHEET 1 AA3 2 ASN A 277 VAL A 279 0
SHEET 2 AA3 2 LYS A 288 VAL A 290 -1 O LYS A 288 N VAL A 279
CISPEP 1 LEU A 133 PRO A 134 0 14.09
CISPEP 2 VAL A 308 PRO A 309 0 -5.24
SITE 1 AC1 25 THR A 176 GLY A 200 ARG A 201 SER A 202
SITE 2 AC1 25 ASN A 204 VAL A 205 HIS A 232 ARG A 233
SITE 3 AC1 25 ALA A 253 ALA A 254 GLY A 255 ILE A 256
SITE 4 AC1 25 VAL A 274 GLY A 275 ILE A 276 GLY A 313
SITE 5 AC1 25 THR A 316 PO4 A 403 HOH A 537 HOH A 544
SITE 6 AC1 25 HOH A 560 HOH A 567 HOH A 592 HOH A 622
SITE 7 AC1 25 HOH A 629
SITE 1 AC2 21 TYR A 84 ASN A 87 LYS A 88 VAL A 131
SITE 2 AC2 21 GLN A 132 LEU A 133 ASP A 155 PHE A 157
SITE 3 AC2 21 ILE A 276 ARG A 278 LEU A 289 PRO A 309
SITE 4 AC2 21 GLY A 310 PRO A 314 HOH A 501 HOH A 515
SITE 5 AC2 21 HOH A 521 HOH A 522 HOH A 530 HOH A 538
SITE 6 AC2 21 HOH A 561
SITE 1 AC3 5 ARG A 201 ARG A 233 NAD A 401 HOH A 537
SITE 2 AC3 5 HOH A 563
CRYST1 74.323 74.323 98.620 90.00 90.00 90.00 I 4 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 0.013455 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013455 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010140 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
