HEADER TRANSFERASE 07-AUG-07 2QV7
TITLE CRYSTAL STRUCTURE OF DIACYLGLYCEROL KINASE DGKB IN COMPLEX WITH ADP
TITLE 2 AND MG
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIACYLGLYCEROL KINASE DGKB;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.7.1.107;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS;
SOURCE 3 GENE: SAR1989;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_STRAIN: METHIONINE AUXOTROPH B834;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PAJ015
KEYWDS ALPHA-BETA DOMAIN 1, BETA SANDWICH DOMAIN 2, PROTEIN-ADP COMPLEX,
KEYWDS 2 TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.J.MILLER,A.JERGA,C.O.ROCK,S.W.WHITE
REVDAT 4 13-JUL-11 2QV7 1 VERSN
REVDAT 3 24-FEB-09 2QV7 1 VERSN
REVDAT 2 05-AUG-08 2QV7 1 JRNL
REVDAT 1 17-JUN-08 2QV7 0
JRNL AUTH D.J.MILLER,A.JERGA,C.O.ROCK,S.W.WHITE
JRNL TITL ANALYSIS OF THE STAPHYLOCOCCUS AUREUS DGKB STRUCTURE REVEALS
JRNL TITL 2 A COMMON CATALYTIC MECHANISM FOR THE SOLUBLE DIACYLGLYCEROL
JRNL TITL 3 KINASES.
JRNL REF STRUCTURE V. 16 1036 2008
JRNL REFN ISSN 0969-2126
JRNL PMID 18611377
JRNL DOI 10.1016/J.STR.2008.03.019
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.17
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 16069
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) : 0.208
REMARK 3 R VALUE (WORKING SET) : 0.206
REMARK 3 FREE R VALUE : 0.246
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 857
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1130
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.34
REMARK 3 BIN R VALUE (WORKING SET) : 0.2180
REMARK 3 BIN FREE R VALUE SET COUNT : 81
REMARK 3 BIN FREE R VALUE : 0.2850
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2324
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 28
REMARK 3 SOLVENT ATOMS : 152
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.14
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : -0.01000
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): 0.312
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.228
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.497
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2393 ; 0.007 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3240 ; 1.122 ; 1.985
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 5.887 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;39.929 ;25.093
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 406 ;14.053 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.523 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 363 ; 0.061 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1801 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1050 ; 0.177 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1583 ; 0.300 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 183 ; 0.107 ; 0.200
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): 23 ; 0.171 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.189 ; 0.200
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): 1542 ; 0.430 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2388 ; 0.676 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 953 ; 1.093 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 852 ; 1.603 ; 4.500
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 : 6
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 1 A 124
REMARK 3 ORIGIN FOR THE GROUP (A): 57.3594 39.6975 21.3913
REMARK 3 T TENSOR
REMARK 3 T11: -0.0960 T22: -0.0549
REMARK 3 T33: -0.1044 T12: -0.0286
REMARK 3 T13: -0.0305 T23: 0.0365
REMARK 3 L TENSOR
REMARK 3 L11: 2.0622 L22: 2.8803
REMARK 3 L33: 1.3444 L12: -1.7480
REMARK 3 L13: -0.2376 L23: 0.1033
REMARK 3 S TENSOR
REMARK 3 S11: 0.1358 S12: -0.0014 S13: -0.0199
REMARK 3 S21: -0.0425 S22: -0.0911 S23: -0.0721
REMARK 3 S31: -0.0260 S32: 0.0218 S33: -0.0447
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 135 A 144
REMARK 3 ORIGIN FOR THE GROUP (A): 81.3782 25.7499 32.2201
REMARK 3 T TENSOR
REMARK 3 T11: -0.1061 T22: 0.2071
REMARK 3 T33: -0.0736 T12: 0.0341
REMARK 3 T13: -0.0068 T23: 0.0912
REMARK 3 L TENSOR
REMARK 3 L11: 15.6810 L22: 3.9168
REMARK 3 L33: 9.4463 L12: -4.5680
REMARK 3 L13: 7.4619 L23: -2.0515
REMARK 3 S TENSOR
REMARK 3 S11: -0.2467 S12: -0.6825 S13: 0.0752
REMARK 3 S21: 0.3456 S22: 0.1075 S23: -0.0115
REMARK 3 S31: -0.2163 S32: 1.0035 S33: 0.1392
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 166 A 200
REMARK 3 RESIDUE RANGE : A 207 A 229
REMARK 3 ORIGIN FOR THE GROUP (A): 80.6206 19.0486 24.3563
REMARK 3 T TENSOR
REMARK 3 T11: -0.0420 T22: -0.0841
REMARK 3 T33: -0.0819 T12: 0.0383
REMARK 3 T13: -0.0131 T23: 0.0724
REMARK 3 L TENSOR
REMARK 3 L11: 6.9970 L22: 1.0319
REMARK 3 L33: 0.3777 L12: -0.8824
REMARK 3 L13: 0.6812 L23: 0.1919
REMARK 3 S TENSOR
REMARK 3 S11: -0.0669 S12: -0.3633 S13: -0.4159
REMARK 3 S21: -0.0507 S22: -0.0118 S23: 0.0378
REMARK 3 S31: 0.2378 S32: 0.0558 S33: 0.0787
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 230 A 249
REMARK 3 ORIGIN FOR THE GROUP (A): 91.7559 22.5470 17.5372
REMARK 3 T TENSOR
REMARK 3 T11: 0.0080 T22: -0.0552
REMARK 3 T33: -0.1495 T12: 0.0769
REMARK 3 T13: 0.0515 T23: 0.0114
REMARK 3 L TENSOR
REMARK 3 L11: 7.3962 L22: 8.6303
REMARK 3 L33: 6.0806 L12: 0.3019
REMARK 3 L13: 1.1521 L23: -2.0601
REMARK 3 S TENSOR
REMARK 3 S11: 0.0492 S12: 0.3618 S13: -0.1648
REMARK 3 S21: -0.2852 S22: 0.0725 S23: 0.2903
REMARK 3 S31: -0.1564 S32: -0.0423 S33: -0.1217
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 250 A 286
REMARK 3 ORIGIN FOR THE GROUP (A): 73.7884 19.2829 29.7515
REMARK 3 T TENSOR
REMARK 3 T11: -0.1043 T22: -0.0193
REMARK 3 T33: -0.1161 T12: 0.0492
REMARK 3 T13: -0.0183 T23: 0.1247
REMARK 3 L TENSOR
REMARK 3 L11: 7.9025 L22: 4.0166
REMARK 3 L33: 2.1110 L12: -1.4924
REMARK 3 L13: 0.3437 L23: 0.4875
REMARK 3 S TENSOR
REMARK 3 S11: -0.1975 S12: -1.1044 S13: -0.5486
REMARK 3 S21: 0.3938 S22: 0.1936 S23: 0.0906
REMARK 3 S31: 0.1500 S32: 0.0248 S33: 0.0040
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 296 A 312
REMARK 3 ORIGIN FOR THE GROUP (A): 64.0648 29.3605 3.5840
REMARK 3 T TENSOR
REMARK 3 T11: 0.0033 T22: 0.1301
REMARK 3 T33: -0.2182 T12: 0.1568
REMARK 3 T13: -0.0567 T23: -0.0350
REMARK 3 L TENSOR
REMARK 3 L11: 10.3742 L22: 17.2624
REMARK 3 L33: 8.7137 L12: -4.1852
REMARK 3 L13: 4.0752 L23: -5.9460
REMARK 3 S TENSOR
REMARK 3 S11: 0.5359 S12: 1.9443 S13: -0.0013
REMARK 3 S21: -1.1273 S22: -0.4027 S23: -0.0158
REMARK 3 S31: 0.0786 S32: 0.5026 S33: -0.1331
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
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 2QV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-07.
REMARK 100 THE RCSB ID CODE IS RCSB044096.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 14-MAR-07
REMARK 200 TEMPERATURE (KELVIN) : 170
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : SI-220
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16997
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 12.200
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.12800
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 8.30
REMARK 200 R MERGE FOR SHELL (I) : 0.43100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT OF
REMARK 200 DGKB
REMARK 200 SOFTWARE USED: DGKB MODEL USED FOR RIGID BODY REFINEMENT
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.93
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: DROP: 0.1 M TRIS PH 8.5, 9% PEG2K MME;
REMARK 280 WELL: 0.1 M TRIS PH 8.5, 18% PEG2K MME, VAPOR DIFFUSION,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2
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+1/2,X+1/2,Z+1/2
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2
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,X,-Z
REMARK 290 8555 -Y,-X,-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 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 61.88000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.88000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.84000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.88000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 61.88000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.84000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 61.88000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.88000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.84000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 61.88000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.88000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 23.84000
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
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 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 47.68000
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 MSE A -21
REMARK 465 GLY A -20
REMARK 465 SER A -19
REMARK 465 SER A -18
REMARK 465 HIS A -17
REMARK 465 HIS A -16
REMARK 465 HIS A -15
REMARK 465 HIS A -14
REMARK 465 HIS A -13
REMARK 465 HIS A -12
REMARK 465 HIS A -11
REMARK 465 SER A -10
REMARK 465 SER A -9
REMARK 465 GLY A -8
REMARK 465 LEU A -7
REMARK 465 VAL A -6
REMARK 465 PRO A -5
REMARK 465 ARG A -4
REMARK 465 VAL A 145
REMARK 465 SER A 146
REMARK 465 TYR A 147
REMARK 465 GLU A 148
REMARK 465 THR A 149
REMARK 465 PRO A 150
REMARK 465 SER A 151
REMARK 465 LYS A 152
REMARK 465 LEU A 153
REMARK 465 LYS A 154
REMARK 465 SER A 155
REMARK 465 ILE A 156
REMARK 465 VAL A 157
REMARK 465 ILE A 313
REMARK 465 GLU A 314
REMARK 465 GLU A 315
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 SER A -2 OG
REMARK 470 HIS A -1 CG ND1 CD2 CE1 NE2
REMARK 470 MSE A 0 CG SE CE
REMARK 470 GLN A 144 CG CD OE1 NE2
REMARK 470 TYR A 162 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 LYS A 165 CG CD CE NZ
REMARK 470 GLN A 267 CG CD OE1 NE2
REMARK 470 ASP A 309 CG OD1 OD2
REMARK 470 ASP A 310 CG OD1 OD2
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 ASN A 129 -105.56 51.09
REMARK 500 LYS A 165 78.99 -102.04
REMARK 500 LEU A 193 144.32 -170.82
REMARK 500 LEU A 198 -65.07 -106.12
REMARK 500 MSE A 202 -155.23 -141.84
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 MG A 501 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 213 O
REMARK 620 2 ASP A 216 OD2 84.6
REMARK 620 3 TYR A 218 O 171.4 89.4
REMARK 620 4 HOH A 582 O 87.3 83.8 98.1
REMARK 620 5 HOH A 531 O 90.9 166.0 96.4 82.8
REMARK 620 6 HOH A 511 O 84.4 98.7 90.5 171.0 94.0
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 500
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2QVL RELATED DB: PDB
REMARK 900 'APO FORM'
DBREF 2QV7 A 1 315 UNP Q6GFF9 Q6GFF9_STAAR 1 315
SEQADV 2QV7 MSE A -21 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 GLY A -20 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 SER A -19 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 SER A -18 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -17 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -16 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -15 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -14 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -13 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -12 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -11 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 SER A -10 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 SER A -9 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 GLY A -8 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 LEU A -7 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 VAL A -6 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 PRO A -5 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 ARG A -4 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 GLY A -3 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 SER A -2 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 HIS A -1 UNP Q6GFF9 EXPRESSION TAG
SEQADV 2QV7 MSE A 0 UNP Q6GFF9 EXPRESSION TAG
SEQRES 1 A 337 MSE GLY SER SER HIS HIS HIS HIS HIS HIS HIS SER SER
SEQRES 2 A 337 GLY LEU VAL PRO ARG GLY SER HIS MSE MSE ARG LYS ARG
SEQRES 3 A 337 ALA ARG ILE ILE TYR ASN PRO THR SER GLY LYS GLU GLN
SEQRES 4 A 337 PHE LYS ARG GLU LEU PRO ASP ALA LEU ILE LYS LEU GLU
SEQRES 5 A 337 LYS ALA GLY TYR GLU THR SER ALA TYR ALA THR GLU LYS
SEQRES 6 A 337 ILE GLY ASP ALA THR LEU GLU ALA GLU ARG ALA MSE HIS
SEQRES 7 A 337 GLU ASN TYR ASP VAL LEU ILE ALA ALA GLY GLY ASP GLY
SEQRES 8 A 337 THR LEU ASN GLU VAL VAL ASN GLY ILE ALA GLU LYS PRO
SEQRES 9 A 337 ASN ARG PRO LYS LEU GLY VAL ILE PRO MSE GLY THR VAL
SEQRES 10 A 337 ASN ASP PHE GLY ARG ALA LEU HIS ILE PRO ASN ASP ILE
SEQRES 11 A 337 MSE GLY ALA LEU ASP VAL ILE ILE GLU GLY HIS SER THR
SEQRES 12 A 337 LYS VAL ASP ILE GLY LYS MSE ASN ASN ARG TYR PHE ILE
SEQRES 13 A 337 ASN LEU ALA ALA GLY GLY GLN LEU THR GLN VAL SER TYR
SEQRES 14 A 337 GLU THR PRO SER LYS LEU LYS SER ILE VAL GLY PRO PHE
SEQRES 15 A 337 ALA TYR TYR ILE LYS GLY PHE GLU MSE LEU PRO GLN MSE
SEQRES 16 A 337 LYS ALA VAL ASP LEU ARG ILE GLU TYR ASP GLY ASN VAL
SEQRES 17 A 337 PHE GLN GLY GLU ALA LEU LEU PHE PHE LEU GLY LEU THR
SEQRES 18 A 337 ASN SER MSE ALA GLY PHE GLU LYS LEU VAL PRO ASP ALA
SEQRES 19 A 337 LYS LEU ASP ASP GLY TYR PHE THR LEU ILE ILE VAL GLU
SEQRES 20 A 337 LYS SER ASN LEU ALA GLU LEU GLY HIS ILE MSE THR LEU
SEQRES 21 A 337 ALA SER ARG GLY GLU HIS THR LYS HIS PRO LYS VAL ILE
SEQRES 22 A 337 TYR GLU LYS ALA LYS ALA ILE ASN ILE SER SER PHE THR
SEQRES 23 A 337 ASP LEU GLN LEU ASN VAL ASP GLY GLU TYR GLY GLY LYS
SEQRES 24 A 337 LEU PRO ALA ASN PHE LEU ASN LEU GLU ARG HIS ILE ASP
SEQRES 25 A 337 VAL PHE ALA PRO ASN ASP ILE VAL ASN GLU GLU LEU ILE
SEQRES 26 A 337 ASN ASN ASP HIS VAL ASP ASP ASN LEU ILE GLU GLU
MODRES 2QV7 MSE A 0 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 1 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 55 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 92 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 109 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 128 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 169 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 173 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 202 MET SELENOMETHIONINE
MODRES 2QV7 MSE A 236 MET SELENOMETHIONINE
HET MSE A 0 5
HET MSE A 1 8
HET MSE A 55 8
HET MSE A 92 8
HET MSE A 109 8
HET MSE A 128 8
HET MSE A 169 8
HET MSE A 173 8
HET MSE A 202 8
HET MSE A 236 8
HET MG A 501 1
HET ADP A 500 27
HETNAM MSE SELENOMETHIONINE
HETNAM MG MAGNESIUM ION
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
FORMUL 1 MSE 10(C5 H11 N O2 SE)
FORMUL 2 MG MG 2+
FORMUL 3 ADP C10 H15 N5 O10 P2
FORMUL 4 HOH *152(H2 O)
HELIX 1 1 GLN A 17 ALA A 32 1 16
HELIX 2 2 GLY A 45 MSE A 55 1 11
HELIX 3 3 GLY A 67 ALA A 79 1 13
HELIX 4 4 ASN A 96 LEU A 102 1 7
HELIX 5 5 ASP A 107 GLY A 118 1 12
HELIX 6 6 GLY A 158 TYR A 162 5 5
HELIX 7 7 MSE A 169 MSE A 173 5 5
HELIX 8 8 ASN A 228 SER A 240 1 13
HELIX 9 9 ARG A 241 GLY A 242 5 2
HELIX 10 10 GLU A 243 HIS A 247 5 5
SHEET 1 A 4 TYR A 34 ALA A 40 0
SHEET 2 A 4 LYS A 3 TYR A 9 1 N LYS A 3 O GLU A 35
SHEET 3 A 4 VAL A 61 GLY A 66 1 O ILE A 63 N ILE A 8
SHEET 4 A 4 LYS A 86 PRO A 91 1 O GLY A 88 N ALA A 64
SHEET 1 B 8 ARG A 131 PHE A 133 0
SHEET 2 B 8 SER A 120 MSE A 128 -1 N MSE A 128 O ARG A 131
SHEET 3 B 8 ALA A 280 PHE A 292 -1 O VAL A 291 N THR A 121
SHEET 4 B 8 ALA A 257 SER A 261 -1 N ILE A 258 O PHE A 282
SHEET 5 B 8 VAL A 176 TYR A 182 -1 N GLU A 181 O ASN A 259
SHEET 6 B 8 ASN A 185 GLY A 197 -1 O PHE A 187 N ILE A 180
SHEET 7 B 8 PHE A 219 GLU A 225 -1 O THR A 220 N GLY A 197
SHEET 8 B 8 VAL A 250 ALA A 255 -1 O ILE A 251 N ILE A 223
SHEET 1 C 9 ARG A 131 PHE A 133 0
SHEET 2 C 9 SER A 120 MSE A 128 -1 N MSE A 128 O ARG A 131
SHEET 3 C 9 ALA A 280 PHE A 292 -1 O VAL A 291 N THR A 121
SHEET 4 C 9 ALA A 257 SER A 261 -1 N ILE A 258 O PHE A 282
SHEET 5 C 9 VAL A 176 TYR A 182 -1 N GLU A 181 O ASN A 259
SHEET 6 C 9 ASN A 185 GLY A 197 -1 O PHE A 187 N ILE A 180
SHEET 7 C 9 LEU A 136 GLY A 140 -1 N ALA A 137 O LEU A 196
SHEET 8 C 9 GLN A 267 VAL A 270 -1 O ASN A 269 N ALA A 138
SHEET 9 C 9 GLU A 273 LYS A 277 -1 O GLU A 273 N VAL A 270
LINK O LYS A 213 MG MG A 501 1555 1555 2.19
LINK OD2 ASP A 216 MG MG A 501 1555 1555 2.34
LINK O TYR A 218 MG MG A 501 1555 1555 2.24
LINK MG MG A 501 O HOH A 582 1555 1555 2.19
LINK MG MG A 501 O HOH A 531 1555 1555 2.38
LINK MG MG A 501 O HOH A 511 1555 1555 2.26
LINK C HIS A -1 N MSE A 0 1555 1555 1.33
LINK C MSE A 0 N MSE A 1 1555 1555 1.33
LINK C MSE A 1 N ARG A 2 1555 1555 1.33
LINK C ALA A 54 N MSE A 55 1555 1555 1.33
LINK C MSE A 55 N HIS A 56 1555 1555 1.33
LINK C PRO A 91 N MSE A 92 1555 1555 1.33
LINK C MSE A 92 N GLY A 93 1555 1555 1.33
LINK C ILE A 108 N MSE A 109 1555 1555 1.33
LINK C MSE A 109 N GLY A 110 1555 1555 1.33
LINK C LYS A 127 N MSE A 128 1555 1555 1.33
LINK C MSE A 128 N ASN A 129 1555 1555 1.33
LINK C GLU A 168 N MSE A 169 1555 1555 1.33
LINK C MSE A 169 N LEU A 170 1555 1555 1.33
LINK C GLN A 172 N MSE A 173 1555 1555 1.33
LINK C MSE A 173 N LYS A 174 1555 1555 1.33
LINK C SER A 201 N MSE A 202 1555 1555 1.33
LINK C MSE A 202 N ALA A 203 1555 1555 1.33
LINK C ILE A 235 N MSE A 236 1555 1555 1.33
LINK C MSE A 236 N THR A 237 1555 1555 1.33
CISPEP 1 LEU A 278 PRO A 279 0 2.84
SITE 1 AC1 6 LYS A 213 ASP A 216 TYR A 218 HOH A 511
SITE 2 AC1 6 HOH A 531 HOH A 582
SITE 1 AC2 17 ASN A 10 THR A 12 SER A 13 GLY A 14
SITE 2 AC2 17 THR A 41 GLU A 42 LYS A 43 ILE A 44
SITE 3 AC2 17 GLY A 66 GLY A 67 GLY A 69 THR A 70
SITE 4 AC2 17 GLU A 73 GLY A 93 THR A 94 HOH A 527
SITE 5 AC2 17 HOH A 625
CRYST1 123.760 123.760 47.680 90.00 90.00 90.00 P 42 21 2 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 0.008080 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008080 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020973 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
