HEADER LIGASE 21-APR-07 2PMF
TITLE THE CRYSTAL STRUCTURE OF A HUMAN GLYCYL-TRNA SYNTHETASE MUTANT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GLYCYL-TRNA SYNTHETASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: GLYCINE--TRNA LIGASE, GLYRS;
COMPND 5 EC: 6.1.1.14;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: GARS;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-DE3;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A(+)
KEYWDS CLASSIIA AMINOACYL-TRNA SYNTHETASE, LIGASE
EXPDTA X-RAY DIFFRACTION
AUTHOR W.XIE
REVDAT 8 03-APR-24 2PMF 1 REMARK
REVDAT 7 21-FEB-24 2PMF 1 REMARK
REVDAT 6 20-OCT-21 2PMF 1 REMARK SEQADV
REVDAT 5 18-OCT-17 2PMF 1 REMARK
REVDAT 4 13-JUL-11 2PMF 1 VERSN
REVDAT 3 24-FEB-09 2PMF 1 VERSN
REVDAT 2 19-JUN-07 2PMF 1 JRNL
REVDAT 1 22-MAY-07 2PMF 0
JRNL AUTH W.XIE,L.A.NANGLE,W.ZHANG,P.SCHIMMEL,X.L.YANG
JRNL TITL LONG-RANGE STRUCTURAL EFFECTS OF A CHARCOT-MARIE- TOOTH
JRNL TITL 2 DISEASE-CAUSING MUTATION IN HUMAN GLYCYL-TRNA SYNTHETASE.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 9976 2007
JRNL REFN ISSN 0027-8424
JRNL PMID 17545306
JRNL DOI 10.1073/PNAS.0703908104
REMARK 2
REMARK 2 RESOLUTION. 2.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.24
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9
REMARK 3 NUMBER OF REFLECTIONS : 24999
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) : 0.233
REMARK 3 R VALUE (WORKING SET) : 0.231
REMARK 3 FREE R VALUE : 0.271
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1272
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) : 2.85
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1614
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.53
REMARK 3 BIN R VALUE (WORKING SET) : 0.2880
REMARK 3 BIN FREE R VALUE SET COUNT : 96
REMARK 3 BIN FREE R VALUE : 0.3980
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4144
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 7
REMARK 3 SOLVENT ATOMS : 202
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.09
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.05000
REMARK 3 B22 (A**2) : -0.05000
REMARK 3 B33 (A**2) : 0.11000
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): 0.559
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.338
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.238
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.878
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4242 ; 0.003 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5727 ; 0.847 ; 1.948
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 519 ; 6.719 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;29.665 ;23.762
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 722 ;15.962 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;14.902 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 616 ; 0.078 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3260 ; 0.002 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2037 ; 0.229 ; 0.300
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2860 ; 0.326 ; 0.500
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 347 ; 0.199 ; 0.500
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): 64 ; 0.200 ; 0.300
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.335 ; 0.500
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): 2651 ; 4.783 ; 3.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4180 ; 7.074 ; 4.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1764 ; 3.341 ; 2.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1547 ; 4.904 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
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 : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 2PMF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-07.
REMARK 100 THE DEPOSITION ID IS D_1000042538.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-JUL-06
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL9-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25080
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 13.80
REMARK 200 R MERGE (I) : 0.06600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5
REMARK 200 DATA REDUNDANCY IN SHELL : 14.00
REMARK 200 R MERGE FOR SHELL (I) : 0.37000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: THE NATIVE T.THERMOPHILUS GLYRS STRUCTURE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.90
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-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 123.40700
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.70600
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.70600
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 185.11050
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.70600
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.70600
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.70350
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.70600
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.70600
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 185.11050
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.70600
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.70600
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.70350
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 123.40700
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 300 REMARK: THE OTHER MONOMER OF THE BIOLOGICAL ASSEMBLY IS GENERATED
REMARK 300 BY THE OPERATION: Y,X+1,-Z
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,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 6120 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 46600 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 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 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 MET A 1
REMARK 465 ASP A 2
REMARK 465 GLY A 3
REMARK 465 ALA A 4
REMARK 465 GLY A 5
REMARK 465 ALA A 6
REMARK 465 GLU A 7
REMARK 465 GLU A 8
REMARK 465 VAL A 9
REMARK 465 LEU A 10
REMARK 465 ALA A 11
REMARK 465 PRO A 12
REMARK 465 LEU A 13
REMARK 465 ARG A 14
REMARK 465 LEU A 15
REMARK 465 ALA A 16
REMARK 465 VAL A 17
REMARK 465 ARG A 18
REMARK 465 GLN A 19
REMARK 465 GLN A 20
REMARK 465 GLY A 21
REMARK 465 ASP A 22
REMARK 465 LEU A 23
REMARK 465 VAL A 24
REMARK 465 ARG A 25
REMARK 465 LYS A 26
REMARK 465 LEU A 27
REMARK 465 LYS A 28
REMARK 465 GLU A 29
REMARK 465 ASP A 30
REMARK 465 LYS A 31
REMARK 465 ALA A 32
REMARK 465 PRO A 33
REMARK 465 GLN A 34
REMARK 465 VAL A 35
REMARK 465 ASP A 36
REMARK 465 VAL A 37
REMARK 465 ASP A 38
REMARK 465 LYS A 39
REMARK 465 ALA A 40
REMARK 465 VAL A 41
REMARK 465 ALA A 42
REMARK 465 GLU A 43
REMARK 465 LEU A 44
REMARK 465 LYS A 45
REMARK 465 ALA A 46
REMARK 465 ARG A 47
REMARK 465 LYS A 48
REMARK 465 ARG A 49
REMARK 465 VAL A 50
REMARK 465 LEU A 51
REMARK 465 GLU A 52
REMARK 465 ALA A 53
REMARK 465 LYS A 54
REMARK 465 GLU A 55
REMARK 465 LEU A 56
REMARK 465 ALA A 57
REMARK 465 LEU A 58
REMARK 465 GLN A 59
REMARK 465 PRO A 60
REMARK 465 LYS A 61
REMARK 465 ASP A 62
REMARK 465 GLU A 382
REMARK 465 MET A 383
REMARK 465 ALA A 384
REMARK 465 HIS A 385
REMARK 465 TYR A 386
REMARK 465 ALA A 421
REMARK 465 THR A 422
REMARK 465 LYS A 423
REMARK 465 VAL A 424
REMARK 465 PRO A 425
REMARK 465 LEU A 426
REMARK 465 VAL A 427
REMARK 465 ALA A 428
REMARK 465 GLU A 429
REMARK 465 LYS A 430
REMARK 465 PRO A 431
REMARK 465 LEU A 432
REMARK 465 LYS A 433
REMARK 465 GLU A 434
REMARK 465 PRO A 435
REMARK 465 LYS A 436
REMARK 465 THR A 437
REMARK 465 VAL A 438
REMARK 465 ASN A 439
REMARK 465 VAL A 440
REMARK 465 VAL A 441
REMARK 465 GLN A 442
REMARK 465 PHE A 443
REMARK 465 GLU A 444
REMARK 465 PRO A 445
REMARK 465 SER A 446
REMARK 465 LYS A 447
REMARK 465 GLY A 448
REMARK 465 ALA A 449
REMARK 465 ILE A 450
REMARK 465 GLY A 451
REMARK 465 LYS A 452
REMARK 465 ALA A 453
REMARK 465 TYR A 454
REMARK 465 LYS A 455
REMARK 465 LYS A 456
REMARK 465 ASP A 457
REMARK 465 ALA A 458
REMARK 465 LYS A 459
REMARK 465 LEU A 460
REMARK 465 VAL A 461
REMARK 465 MET A 462
REMARK 465 GLU A 463
REMARK 465 TYR A 464
REMARK 465 LEU A 465
REMARK 465 ALA A 466
REMARK 465 ILE A 467
REMARK 465 CYS A 468
REMARK 465 ASP A 469
REMARK 465 GLU A 470
REMARK 465 CYS A 471
REMARK 465 TYR A 472
REMARK 465 ILE A 473
REMARK 465 THR A 474
REMARK 465 GLU A 475
REMARK 465 MET A 476
REMARK 465 GLU A 477
REMARK 465 MET A 478
REMARK 465 LEU A 479
REMARK 465 LEU A 480
REMARK 465 ASN A 481
REMARK 465 GLU A 482
REMARK 465 LYS A 483
REMARK 465 GLY A 484
REMARK 465 GLU A 485
REMARK 465 PHE A 486
REMARK 465 THR A 487
REMARK 465 ILE A 488
REMARK 465 GLU A 489
REMARK 465 THR A 490
REMARK 465 GLU A 491
REMARK 465 GLY A 492
REMARK 465 LYS A 493
REMARK 465 THR A 494
REMARK 465 PHE A 495
REMARK 465 GLN A 496
REMARK 465 LEU A 497
REMARK 465 THR A 498
REMARK 465 LYS A 499
REMARK 465 ASP A 500
REMARK 465 MET A 501
REMARK 465 ILE A 502
REMARK 465 ASN A 503
REMARK 465 VAL A 504
REMARK 465 LYS A 505
REMARK 465 GLN A 675
REMARK 465 GLU A 676
REMARK 465 THR A 677
REMARK 465 GLY A 678
REMARK 465 LYS A 679
REMARK 465 LYS A 680
REMARK 465 GLU A 681
REMARK 465 THR A 682
REMARK 465 ILE A 683
REMARK 465 GLU A 684
REMARK 465 GLU A 685
REMARK 465 LEU A 686
REMARK 465 GLU A 687
REMARK 465 HIS A 688
REMARK 465 HIS A 689
REMARK 465 HIS A 690
REMARK 465 HIS A 691
REMARK 465 HIS A 692
REMARK 465 HIS A 693
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 ASP A 63 CG OD1 OD2
REMARK 470 ILE A 64 CG1 CG2 CD1
REMARK 470 ARG A 506 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 508 CG CD OE1 NE2
REMARK 470 THR A 510 OG1 CG2
REMARK 470 LEU A 511 CG CD1 CD2
REMARK 470 TYR A 512 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 VAL A 513 CG1 CG2
REMARK 470 GLU A 673 CG CD OE1 OE2
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 ASN A 154 N GLU A 156 2.00
REMARK 500 O ASN A 657 N ASN A 659 2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 OG SER A 178 O ARG A 668 7455 2.14
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 ILE A 64 -100.69 -92.04
REMARK 500 SER A 138 -65.79 -126.91
REMARK 500 PHE A 144 137.09 157.23
REMARK 500 ASP A 174 104.25 -163.98
REMARK 500 LYS A 175 69.00 -119.53
REMARK 500 GLN A 198 -94.27 -50.82
REMARK 500 GLU A 199 -59.64 10.67
REMARK 500 PRO A 212 -75.56 -55.47
REMARK 500 THR A 214 139.80 -35.78
REMARK 500 ASN A 278 78.30 -69.79
REMARK 500 SER A 281 78.30 -151.41
REMARK 500 ARG A 283 39.70 -154.19
REMARK 500 LYS A 306 41.51 -95.78
REMARK 500 SER A 329 46.51 -106.64
REMARK 500 TYR A 413 -158.86 -117.66
REMARK 500 LEU A 511 151.12 -44.25
REMARK 500 TYR A 512 22.30 90.47
REMARK 500 GLN A 547 87.27 -38.68
REMARK 500 SER A 552 54.59 -93.96
REMARK 500 SER A 568 126.06 -25.38
REMARK 500 GLN A 569 109.76 -41.79
REMARK 500 GLN A 571 -3.95 -55.53
REMARK 500 ASP A 595 55.03 -96.77
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 LYS A 143 PHE A 144 137.73
REMARK 500 LYS A 175 LYS A 176 145.13
REMARK 500 LEU A 265 PRO A 266 121.68
REMARK 500 HIS A 378 MET A 379 -148.04
REMARK 500 THR A 626 PRO A 627 129.53
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 901
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 801
DBREF 2PMF A 1 685 UNP P41250 SYG_HUMAN 55 739
SEQADV 2PMF ARG A 526 UNP P41250 GLY 580 ENGINEERED MUTATION
SEQADV 2PMF LEU A 686 UNP P41250 CLONING ARTIFACT
SEQADV 2PMF GLU A 687 UNP P41250 CLONING ARTIFACT
SEQADV 2PMF HIS A 688 UNP P41250 CLONING ARTIFACT
SEQADV 2PMF HIS A 689 UNP P41250 CLONING ARTIFACT
SEQADV 2PMF HIS A 690 UNP P41250 CLONING ARTIFACT
SEQADV 2PMF HIS A 691 UNP P41250 CLONING ARTIFACT
SEQADV 2PMF HIS A 692 UNP P41250 CLONING ARTIFACT
SEQADV 2PMF HIS A 693 UNP P41250 CLONING ARTIFACT
SEQRES 1 A 693 MET ASP GLY ALA GLY ALA GLU GLU VAL LEU ALA PRO LEU
SEQRES 2 A 693 ARG LEU ALA VAL ARG GLN GLN GLY ASP LEU VAL ARG LYS
SEQRES 3 A 693 LEU LYS GLU ASP LYS ALA PRO GLN VAL ASP VAL ASP LYS
SEQRES 4 A 693 ALA VAL ALA GLU LEU LYS ALA ARG LYS ARG VAL LEU GLU
SEQRES 5 A 693 ALA LYS GLU LEU ALA LEU GLN PRO LYS ASP ASP ILE VAL
SEQRES 6 A 693 ASP ARG ALA LYS MET GLU ASP THR LEU LYS ARG ARG PHE
SEQRES 7 A 693 PHE TYR ASP GLN ALA PHE ALA ILE TYR GLY GLY VAL SER
SEQRES 8 A 693 GLY LEU TYR ASP PHE GLY PRO VAL GLY CYS ALA LEU LYS
SEQRES 9 A 693 ASN ASN ILE ILE GLN THR TRP ARG GLN HIS PHE ILE GLN
SEQRES 10 A 693 GLU GLU GLN ILE LEU GLU ILE ASP CYS THR MET LEU THR
SEQRES 11 A 693 PRO GLU PRO VAL LEU LYS THR SER GLY HIS VAL ASP LYS
SEQRES 12 A 693 PHE ALA ASP PHE MET VAL LYS ASP VAL LYS ASN GLY GLU
SEQRES 13 A 693 CYS PHE ARG ALA ASP HIS LEU LEU LYS ALA HIS LEU GLN
SEQRES 14 A 693 LYS LEU MET SER ASP LYS LYS CYS SER VAL GLU LYS LYS
SEQRES 15 A 693 SER GLU MET GLU SER VAL LEU ALA GLN LEU ASP ASN TYR
SEQRES 16 A 693 GLY GLN GLN GLU LEU ALA ASP LEU PHE VAL ASN TYR ASN
SEQRES 17 A 693 VAL LYS SER PRO ILE THR GLY ASN ASP LEU SER PRO PRO
SEQRES 18 A 693 VAL SER PHE ASN LEU MET PHE LYS THR PHE ILE GLY PRO
SEQRES 19 A 693 GLY GLY ASN MET PRO GLY TYR LEU ARG PRO GLU THR ALA
SEQRES 20 A 693 GLN GLY ILE PHE LEU ASN PHE LYS ARG LEU LEU GLU PHE
SEQRES 21 A 693 ASN GLN GLY LYS LEU PRO PHE ALA ALA ALA GLN ILE GLY
SEQRES 22 A 693 ASN SER PHE ARG ASN GLU ILE SER PRO ARG SER GLY LEU
SEQRES 23 A 693 ILE ARG VAL ARG GLU PHE THR MET ALA GLU ILE GLU HIS
SEQRES 24 A 693 PHE VAL ASP PRO SER GLU LYS ASP HIS PRO LYS PHE GLN
SEQRES 25 A 693 ASN VAL ALA ASP LEU HIS LEU TYR LEU TYR SER ALA LYS
SEQRES 26 A 693 ALA GLN VAL SER GLY GLN SER ALA ARG LYS MET ARG LEU
SEQRES 27 A 693 GLY ASP ALA VAL GLU GLN GLY VAL ILE ASN ASN THR VAL
SEQRES 28 A 693 LEU GLY TYR PHE ILE GLY ARG ILE TYR LEU TYR LEU THR
SEQRES 29 A 693 LYS VAL GLY ILE SER PRO ASP LYS LEU ARG PHE ARG GLN
SEQRES 30 A 693 HIS MET GLU ASN GLU MET ALA HIS TYR ALA CYS ASP CYS
SEQRES 31 A 693 TRP ASP ALA GLU SER LYS THR SER TYR GLY TRP ILE GLU
SEQRES 32 A 693 ILE VAL GLY CYS ALA ASP ARG SER CYS TYR ASP LEU SER
SEQRES 33 A 693 CYS HIS ALA ARG ALA THR LYS VAL PRO LEU VAL ALA GLU
SEQRES 34 A 693 LYS PRO LEU LYS GLU PRO LYS THR VAL ASN VAL VAL GLN
SEQRES 35 A 693 PHE GLU PRO SER LYS GLY ALA ILE GLY LYS ALA TYR LYS
SEQRES 36 A 693 LYS ASP ALA LYS LEU VAL MET GLU TYR LEU ALA ILE CYS
SEQRES 37 A 693 ASP GLU CYS TYR ILE THR GLU MET GLU MET LEU LEU ASN
SEQRES 38 A 693 GLU LYS GLY GLU PHE THR ILE GLU THR GLU GLY LYS THR
SEQRES 39 A 693 PHE GLN LEU THR LYS ASP MET ILE ASN VAL LYS ARG PHE
SEQRES 40 A 693 GLN LYS THR LEU TYR VAL GLU GLU VAL VAL PRO ASN VAL
SEQRES 41 A 693 ILE GLU PRO SER PHE ARG LEU GLY ARG ILE MET TYR THR
SEQRES 42 A 693 VAL PHE GLU HIS THR PHE HIS VAL ARG GLU GLY ASP GLU
SEQRES 43 A 693 GLN ARG THR PHE PHE SER PHE PRO ALA VAL VAL ALA PRO
SEQRES 44 A 693 PHE LYS CYS SER VAL LEU PRO LEU SER GLN ASN GLN GLU
SEQRES 45 A 693 PHE MET PRO PHE VAL LYS GLU LEU SER GLU ALA LEU THR
SEQRES 46 A 693 ARG HIS GLY VAL SER HIS LYS VAL ASP ASP SER SER GLY
SEQRES 47 A 693 SER ILE GLY ARG ARG TYR ALA ARG THR ASP GLU ILE GLY
SEQRES 48 A 693 VAL ALA PHE GLY VAL THR ILE ASP PHE ASP THR VAL ASN
SEQRES 49 A 693 LYS THR PRO HIS THR ALA THR LEU ARG ASP ARG ASP SER
SEQRES 50 A 693 MET ARG GLN ILE ARG ALA GLU ILE SER GLU LEU PRO SER
SEQRES 51 A 693 ILE VAL GLN ASP LEU ALA ASN GLY ASN ILE THR TRP ALA
SEQRES 52 A 693 ASP VAL GLU ALA ARG TYR PRO LEU PHE GLU GLY GLN GLU
SEQRES 53 A 693 THR GLY LYS LYS GLU THR ILE GLU GLU LEU GLU HIS HIS
SEQRES 54 A 693 HIS HIS HIS HIS
HET CL A 901 1
HET GOL A 801 6
HETNAM CL CHLORIDE ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 CL CL 1-
FORMUL 3 GOL C3 H8 O3
FORMUL 4 HOH *202(H2 O)
HELIX 1 1 ASP A 66 ARG A 77 1 12
HELIX 2 2 PHE A 84 GLY A 88 5 5
HELIX 3 3 GLY A 97 PHE A 115 1 19
HELIX 4 4 PHE A 115 GLN A 120 1 6
HELIX 5 5 GLU A 132 THR A 137 1 6
HELIX 6 6 ALA A 160 SER A 173 1 14
HELIX 7 7 SER A 178 ALA A 190 1 13
HELIX 8 8 GLN A 191 TYR A 195 5 5
HELIX 9 9 GLY A 196 TYR A 207 1 12
HELIX 10 10 THR A 246 LEU A 252 1 7
HELIX 11 11 ASN A 253 ASN A 261 1 9
HELIX 12 12 LYS A 310 VAL A 314 5 5
HELIX 13 13 SER A 323 SER A 329 1 7
HELIX 14 14 LEU A 338 GLN A 344 1 7
HELIX 15 15 ASN A 349 GLY A 367 1 19
HELIX 16 16 SER A 369 ASP A 371 5 3
HELIX 17 17 ASP A 414 ARG A 420 1 7
HELIX 18 18 LEU A 527 THR A 538 1 12
HELIX 19 19 PHE A 573 HIS A 587 1 15
HELIX 20 20 SER A 599 ILE A 610 1 12
HELIX 21 21 ASP A 619 LYS A 625 1 7
HELIX 22 22 GLU A 647 ASN A 657 1 11
HELIX 23 23 THR A 661 TYR A 669 1 9
SHEET 1 A 2 TYR A 80 GLN A 82 0
SHEET 2 A 2 TYR A 94 PHE A 96 -1 O ASP A 95 N ASP A 81
SHEET 1 B 9 LEU A 122 GLU A 123 0
SHEET 2 B 9 PRO A 266 PHE A 276 1 O ALA A 268 N LEU A 122
SHEET 3 B 9 GLU A 291 VAL A 301 -1 O GLU A 298 N ALA A 269
SHEET 4 B 9 ASN A 519 ARG A 526 -1 O PHE A 525 N ALA A 295
SHEET 5 B 9 GLY A 400 ARG A 410 -1 N GLY A 406 O SER A 524
SHEET 6 B 9 ASP A 389 THR A 397 -1 N ALA A 393 O VAL A 405
SHEET 7 B 9 LEU A 373 GLN A 377 -1 N ARG A 376 O ASP A 392
SHEET 8 B 9 HIS A 318 TYR A 322 1 N TYR A 322 O PHE A 375
SHEET 9 B 9 ARG A 334 ARG A 337 -1 O ARG A 334 N LEU A 321
SHEET 1 C 3 LEU A 129 PRO A 131 0
SHEET 2 C 3 PRO A 239 LEU A 242 -1 O TYR A 241 N THR A 130
SHEET 3 C 3 LYS A 229 PHE A 231 -1 N THR A 230 O GLY A 240
SHEET 1 D 3 PHE A 158 ARG A 159 0
SHEET 2 D 3 ALA A 145 VAL A 149 -1 N VAL A 149 O PHE A 158
SHEET 3 D 3 VAL A 222 ASN A 225 -1 O VAL A 222 N MET A 148
SHEET 1 E 2 GLN A 508 THR A 510 0
SHEET 2 E 2 GLU A 514 VAL A 516 -1 O VAL A 516 N GLN A 508
SHEET 1 F 2 PHE A 539 VAL A 541 0
SHEET 2 F 2 THR A 549 PHE A 551 -1 O PHE A 550 N HIS A 540
SHEET 1 G 6 HIS A 591 VAL A 593 0
SHEET 2 G 6 CYS A 562 PRO A 566 1 N CYS A 562 O LYS A 592
SHEET 3 G 6 PHE A 614 ILE A 618 1 O VAL A 616 N LEU A 565
SHEET 4 G 6 THR A 629 ASP A 634 -1 O ARG A 633 N GLY A 615
SHEET 5 G 6 GLN A 640 GLU A 644 -1 O ILE A 641 N LEU A 632
SHEET 6 G 6 LEU A 671 PHE A 672 -1 O PHE A 672 N GLN A 640
CISPEP 1 THR A 214 GLY A 215 0 1.72
SITE 1 AC1 4 ARG A 526 GLY A 528 ARG A 529 HOH A1103
SITE 1 AC2 7 ASP A 621 THR A 622 LYS A 625 PRO A 627
SITE 2 AC2 7 THR A 629 ARG A 642 HOH A 980
CRYST1 91.412 91.412 246.814 90.00 90.00 90.00 P 43 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 0.010939 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010939 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004052 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
