HEADER VIRAL PROTEIN/IMMUNE SYSTEM 27-JAN-15 4XVS
TITLE CRYSTAL STRUCTURE OF HIV-1 DONOR 45 D45-01DG5 COREE GP120 WITH
TITLE 2 ANTIBODY 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653
TITLE 3 (VRC07_1995)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VRC07_1995 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-
COMPND 3 110653 HEAVY CHAIN;
COMPND 4 CHAIN: H;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 LIGHT
COMPND 8 CHAIN;
COMPND 9 CHAIN: L;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: DONOR 45 01DG5 COREE GP120;
COMPND 13 CHAIN: G;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_TAXID: 9606;
SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: 293F;
SOURCE 7 MOL_ID: 2;
SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 9 ORGANISM_TAXID: 9606;
SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: 293F;
SOURCE 13 MOL_ID: 3;
SOURCE 14 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 15 ORGANISM_TAXID: 11676;
SOURCE 16 VARIANT: 01DG5;
SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 19 EXPRESSION_SYSTEM_CELL_LINE: 293F
KEYWDS HIV-1 ANTIBODYOMICS NEUTRALIZING ANTIBODY GERMLINE BINDING, VIRAL
KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.G.JOYCE,J.R.MASCOLA,P.D.KWONG
REVDAT 5 16-OCT-24 4XVS 1 REMARK
REVDAT 4 27-SEP-23 4XVS 1 HETSYN
REVDAT 3 29-JUL-20 4XVS 1 COMPND REMARK HETNAM LINK
REVDAT 3 2 1 SITE
REVDAT 2 27-JUL-16 4XVS 1 REMARK
REVDAT 1 06-MAY-15 4XVS 0
JRNL AUTH X.WU,Z.ZHANG,C.A.SCHRAMM,M.G.JOYCE,Y.DO KWON,T.ZHOU,Z.SHENG,
JRNL AUTH 2 B.ZHANG,S.O'DELL,K.MCKEE,I.S.GEORGIEV,G.Y.CHUANG,N.S.LONGO,
JRNL AUTH 3 R.M.LYNCH,K.O.SAUNDERS,C.SOTO,S.SRIVATSAN,Y.YANG,R.T.BAILER,
JRNL AUTH 4 M.K.LOUDER,J.C.MULLIKIN,M.CONNORS,P.D.KWONG,J.R.MASCOLA,
JRNL AUTH 5 L.SHAPIRO
JRNL TITL MATURATION AND DIVERSITY OF THE VRC01-ANTIBODY LINEAGE OVER
JRNL TITL 2 15 YEARS OF CHRONIC HIV-1 INFECTION.
JRNL REF CELL V. 161 470 2015
JRNL REFN ISSN 1097-4172
JRNL PMID 25865483
JRNL DOI 10.1016/J.CELL.2015.03.004
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.10.0
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.82
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5
REMARK 3 NUMBER OF REFLECTIONS : 69542
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) : 0.195
REMARK 3 R VALUE (WORKING SET) : 0.194
REMARK 3 FREE R VALUE : 0.214
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050
REMARK 3 FREE R VALUE TEST SET COUNT : 3514
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.95
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.45
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4644
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2202
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4430
REMARK 3 BIN R VALUE (WORKING SET) : 0.2186
REMARK 3 BIN FREE R VALUE : 0.2528
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.61
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 214
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6046
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 111
REMARK 3 SOLVENT ATOMS : 626
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.50
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.86390
REMARK 3 B22 (A**2) : -1.56640
REMARK 3 B33 (A**2) : 0.70250
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.253
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.160
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.133
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.151
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.130
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 6287 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 8549 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 2165 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 153 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 912 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 6287 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 860 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 7094 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.02
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.85
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.61
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { H|1 - H|228 H|301 - H|495 }
REMARK 3 ORIGIN FOR THE GROUP (A): 7.1956 32.7245 -13.6074
REMARK 3 T TENSOR
REMARK 3 T11: -0.0384 T22: -0.0513
REMARK 3 T33: -0.0416 T12: -0.0193
REMARK 3 T13: 0.0313 T23: 0.0136
REMARK 3 L TENSOR
REMARK 3 L11: 0.9187 L22: 0.6254
REMARK 3 L33: 0.8900 L12: 0.4324
REMARK 3 L13: 0.5801 L23: 0.4926
REMARK 3 S TENSOR
REMARK 3 S11: -0.0756 S12: 0.0156 S13: 0.0634
REMARK 3 S21: -0.0789 S22: 0.0271 S23: -0.0983
REMARK 3 S31: -0.1408 S32: 0.0820 S33: 0.0485
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: { L|3 - L|216 L|301 - L|476 }
REMARK 3 ORIGIN FOR THE GROUP (A): -1.1324 32.8099 3.1914
REMARK 3 T TENSOR
REMARK 3 T11: -0.0340 T22: -0.0426
REMARK 3 T33: -0.0187 T12: 0.0052
REMARK 3 T13: -0.0070 T23: 0.0046
REMARK 3 L TENSOR
REMARK 3 L11: 0.6519 L22: 0.5965
REMARK 3 L33: 0.4203 L12: 0.3336
REMARK 3 L13: 0.2377 L23: 0.4391
REMARK 3 S TENSOR
REMARK 3 S11: -0.0043 S12: -0.0594 S13: 0.1168
REMARK 3 S21: -0.0242 S22: -0.0053 S23: -0.0120
REMARK 3 S31: -0.0714 S32: -0.0705 S33: 0.0095
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: { G|44 - G|493 G|601 - G|608 G|701 - G|955 }
REMARK 3 ORIGIN FOR THE GROUP (A): -16.3484 6.4766 -43.3132
REMARK 3 T TENSOR
REMARK 3 T11: -0.0699 T22: -0.0315
REMARK 3 T33: -0.1232 T12: 0.0141
REMARK 3 T13: 0.0069 T23: -0.0175
REMARK 3 L TENSOR
REMARK 3 L11: 0.7082 L22: 1.3683
REMARK 3 L33: 1.0127 L12: 0.1719
REMARK 3 L13: -0.4273 L23: 0.2712
REMARK 3 S TENSOR
REMARK 3 S11: -0.0660 S12: 0.1144 S13: -0.0628
REMARK 3 S21: -0.1586 S22: -0.0751 S23: -0.0095
REMARK 3 S31: 0.0137 S32: -0.1203 S33: 0.1411
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4XVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-15.
REMARK 100 THE DEPOSITION ID IS D_1000206374.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 02-APR-13
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 : 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
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69542
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 27.820
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : 0.15000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.90000
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: PHASER
REMARK 200 STARTING MODEL: 4XVT
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.04
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA CACODYLATE PH 6.5, 0.2 M
REMARK 280 NAACETATE, 6 % PEG 8000, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 294K
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 33.82050
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 100.27300
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.66700
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 100.27300
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.82050
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.66700
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 8250 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 35570 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, G
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 GLY G 318
REMARK 465 GLY G 319
REMARK 465 SER G 320
REMARK 465 GLY G 321
REMARK 465 SER G 322
REMARK 465 GLY G 323
REMARK 465 ASP G 401
REMARK 465 THR G 402
REMARK 465 GLU G 403
REMARK 465 VAL G 404
REMARK 465 VAL G 405
REMARK 465 ASN G 406
REMARK 465 ASN G 407
REMARK 465 THR G 408
REMARK 465 GLU G 409
REMARK 465 LYS G 410
REMARK 465 GLY G 494
REMARK 465 SER G 495
REMARK 465 LEU G 496
REMARK 465 GLU G 497
REMARK 465 VAL G 498
REMARK 465 LEU G 499
REMARK 465 PHE G 500
REMARK 465 GLN G 501
REMARK 465 GLY G 502
REMARK 465 PRO G 503
REMARK 465 GLY G 504
REMARK 465 HIS G 505
REMARK 465 HIS G 506
REMARK 465 HIS G 507
REMARK 465 HIS G 508
REMARK 465 HIS G 509
REMARK 465 HIS G 510
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 GLU L 3 CG CD OE1 OE2
REMARK 470 ASN G 398 CG OD1 ND2
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 CG ASN G 362 C1 NAG G 606 2.13
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 SER H 142 41.32 -89.19
REMARK 500 TYR L 91 -128.89 54.54
REMARK 500 LYS L 171 -60.73 -100.85
REMARK 500 LYS L 192 -63.82 -106.60
REMARK 500 ASN G 80 78.85 -118.91
REMARK 500 GLN G 258 -61.54 69.42
REMARK 500 GLU G 268 -98.03 -101.16
REMARK 500 ASN G 276 100.94 -161.47
REMARK 500 ASN G 392 66.48 -158.28
REMARK 500 THR G 465 13.45 55.01
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 H 452 DISTANCE = 6.18 ANGSTROMS
REMARK 525 HOH H 467 DISTANCE = 8.64 ANGSTROMS
REMARK 525 HOH H 471 DISTANCE = 8.04 ANGSTROMS
REMARK 525 HOH H 479 DISTANCE = 8.66 ANGSTROMS
REMARK 525 HOH G 831 DISTANCE = 6.39 ANGSTROMS
REMARK 525 HOH G 852 DISTANCE = 10.00 ANGSTROMS
REMARK 525 HOH G 885 DISTANCE = 7.65 ANGSTROMS
REMARK 525 HOH G 909 DISTANCE = 8.29 ANGSTROMS
REMARK 525 HOH G 953 DISTANCE = 9.01 ANGSTROMS
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 NAG G 607
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4XVT RELATED DB: PDB
DBREF 4XVS H 1 228 PDB 4XVS 4XVS 1 228
DBREF 4XVS L 3 216 PDB 4XVS 4XVS 3 216
DBREF 4XVS G 44 510 PDB 4XVS 4XVS 44 510
SEQRES 1 H 228 GLN VAL GLN LEU LEU GLN SER GLY ALA GLN VAL LYS LYS
SEQRES 2 H 228 THR GLY ALA SER MET ARG ILE SER CYS LYS THR SER GLY
SEQRES 3 H 228 TYR THR PHE LEU ASN CYS PRO ILE ASN TRP VAL ARG GLN
SEQRES 4 H 228 ALA PRO GLY ARG GLY LEU GLU TRP MET GLY TRP MET LYS
SEQRES 5 H 228 PRO ARG GLY GLY ALA VAL ASN TYR PRO GLN LYS PHE GLN
SEQRES 6 H 228 GLY ARG VAL THR MET THR ARG ASP MET SER THR ASP THR
SEQRES 7 H 228 ALA PHE LEU ASP MET SER ASN LEU ARG SER ASP ASP THR
SEQRES 8 H 228 ALA VAL TYR PHE CYS ALA ARG GLY LYS TYR CYS THR ALA
SEQRES 9 H 228 SER ASP TYR TYR ASN TRP ASP PHE GLU HIS TRP GLY ARG
SEQRES 10 H 228 GLY THR LEU VAL THR VAL SER SER PRO ALA THR LYS GLY
SEQRES 11 H 228 PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR
SEQRES 12 H 228 SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP
SEQRES 13 H 228 TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY
SEQRES 14 H 228 ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU
SEQRES 15 H 228 GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR
SEQRES 16 H 228 VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS
SEQRES 17 H 228 ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS
SEQRES 18 H 228 LYS VAL GLU PRO LYS SER CYS
SEQRES 1 L 210 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU
SEQRES 2 L 210 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG THR SER
SEQRES 3 L 210 GLN TYR GLY SER LEU ALA TRP TYR GLN GLN ARG PRO GLY
SEQRES 4 L 210 GLN ALA PRO ARG LEU VAL ILE TYR GLY GLY SER SER ARG
SEQRES 5 L 210 ALA THR GLY ILE PRO ASP ARG PHE THR GLY SER ARG SER
SEQRES 6 L 210 GLY ALA ASP TYR THR LEU THR ILE ASN ARG LEU GLU PRO
SEQRES 7 L 210 GLU ASP PHE GLY ILE TYR TYR CYS GLN GLN TYR GLU PHE
SEQRES 8 L 210 PHE GLY GLN GLY THR LYS VAL GLU VAL ASP ILE LYS ARG
SEQRES 9 L 210 THR VAL ALA ALA PRO SER VAL PHE ILE PHE PRO PRO SER
SEQRES 10 L 210 ASP GLU GLN LEU LYS SER GLY THR ALA SER VAL VAL CYS
SEQRES 11 L 210 LEU LEU ASN ASN PHE TYR PRO ARG GLU ALA LYS VAL GLN
SEQRES 12 L 210 TRP LYS VAL ASP ASN ALA LEU GLN SER GLY ASN SER GLN
SEQRES 13 L 210 GLU SER VAL THR GLU GLN ASP SER LYS ASP SER THR TYR
SEQRES 14 L 210 SER LEU SER SER THR LEU THR LEU SER LYS ALA ASP TYR
SEQRES 15 L 210 GLU LYS HIS LYS VAL TYR ALA CYS GLU VAL THR HIS GLN
SEQRES 16 L 210 GLY LEU ALA SER PRO VAL THR LYS SER PHE ASN ARG GLY
SEQRES 17 L 210 GLU CYS
SEQRES 1 G 375 VAL TRP LYS GLU ALA THR ALA THR LEU PHE CYS ALA SER
SEQRES 2 G 375 ASP ALA LYS ALA TYR GLU THR GLU VAL HIS ASN VAL TRP
SEQRES 3 G 375 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN
SEQRES 4 G 375 GLU VAL VAL LEU GLU ASN VAL THR GLU ASN PHE ASN MET
SEQRES 5 G 375 TRP LYS ASN ASN MET VAL GLU GLN MET HIS GLU ASP ILE
SEQRES 6 G 375 ILE SER LEU TRP ASP GLN SER LEU LYS PRO CYS VAL LYS
SEQRES 7 G 375 LEU THR GLY GLY SER VAL ILE THR GLN ALA CYS PRO LYS
SEQRES 8 G 375 ILE SER PHE GLU PRO ILE PRO ILE HIS TYR CYS ALA PRO
SEQRES 9 G 375 ALA GLY PHE ALA ILE LEU LYS CYS ASN ASP LYS LYS PHE
SEQRES 10 G 375 ASN GLY THR GLY PRO CYS THR ASN VAL SER THR VAL GLN
SEQRES 11 G 375 CYS THR HIS GLY ILE ARG PRO VAL VAL SER THR GLN LEU
SEQRES 12 G 375 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE VAL ILE
SEQRES 13 G 375 ARG SER GLU ASN ILE LYS ASP ASN ALA LYS ILE ILE ILE
SEQRES 14 G 375 VAL GLN LEU ASN GLU THR VAL GLU ILE ASN CYS THR ARG
SEQRES 15 G 375 PRO ASN ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG
SEQRES 16 G 375 GLN ALA HIS CYS ASN ILE SER LYS ALA LYS TRP GLU ASN
SEQRES 17 G 375 THR LEU LYS GLN ILE ALA ARG LYS LEU ARG GLU HIS PHE
SEQRES 18 G 375 LYS ASN GLU THR ILE ALA PHE ASN GLN SER SER GLY GLY
SEQRES 19 G 375 ASP PRO GLU ILE VAL MET HIS SER PHE ASN CYS GLY GLY
SEQRES 20 G 375 GLU PHE PHE TYR CYS ASN SER THR GLN LEU PHE ASN SER
SEQRES 21 G 375 THR TRP THR TRP ASN ASP THR GLU VAL VAL ASN ASN THR
SEQRES 22 G 375 GLU LYS ASN ILE ASN ILE THR LEU PRO CYS ARG ILE LYS
SEQRES 23 G 375 GLN ILE ILE ASN MET TRP GLN GLU VAL GLY LYS ALA MET
SEQRES 24 G 375 TYR ALA PRO PRO ILE LYS GLY GLN ILE ARG CYS SER SER
SEQRES 25 G 375 ASN ILE THR GLY LEU LEU LEU THR ARG ASP GLY GLY SER
SEQRES 26 G 375 SER THR ASN GLY THR THR GLU THR PHE ARG PRO GLY GLY
SEQRES 27 G 375 GLY ASP MET ARG ASP ASN TRP ARG SER GLU LEU TYR LYS
SEQRES 28 G 375 TYR LYS VAL VAL LYS ILE GLU GLY SER LEU GLU VAL LEU
SEQRES 29 G 375 PHE GLN GLY PRO GLY HIS HIS HIS HIS HIS HIS
HET NAG G 601 14
HET NAG G 602 14
HET NAG G 603 14
HET NAG G 604 14
HET NAG G 605 14
HET NAG G 606 14
HET NAG G 607 13
HET NAG G 608 14
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA-
HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO-
HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE
FORMUL 4 NAG 8(C8 H15 N O6)
FORMUL 12 HOH *626(H2 O)
HELIX 1 AA1 THR H 28 CYS H 32 5 5
HELIX 2 AA2 PRO H 61 GLN H 65 5 5
HELIX 3 AA3 ARG H 87 THR H 91 5 5
HELIX 4 AA4 SER H 168 ALA H 170 5 3
HELIX 5 AA5 SER H 199 LEU H 201 5 3
HELIX 6 AA6 LYS H 213 ASN H 216 5 4
HELIX 7 AA7 GLU L 79 PHE L 83 5 5
HELIX 8 AA8 SER L 123 SER L 129 1 7
HELIX 9 AA9 LYS L 185 GLU L 189 1 5
HELIX 10 AB1 GLU G 64 ALA G 73 1 10
HELIX 11 AB2 ASN G 98 LEU G 116 1 19
HELIX 12 AB3 LYS G 335 ARG G 350 1 16
HELIX 13 AB4 ASP G 368 MET G 373 1 6
HELIX 14 AB5 SER G 387 PHE G 391 5 5
HELIX 15 AB6 MET G 476 TYR G 485 1 10
SHEET 1 AA1 4 GLN H 3 GLN H 6 0
SHEET 2 AA1 4 MET H 18 SER H 25 -1 O LYS H 23 N LEU H 5
SHEET 3 AA1 4 THR H 78 MET H 83 -1 O ALA H 79 N CYS H 22
SHEET 4 AA1 4 VAL H 68 ASP H 73 -1 N THR H 71 O PHE H 80
SHEET 1 AA2 6 GLN H 10 LYS H 13 0
SHEET 2 AA2 6 THR H 119 SER H 124 1 O THR H 122 N LYS H 12
SHEET 3 AA2 6 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 119
SHEET 4 AA2 6 ILE H 34 GLN H 39 -1 N VAL H 37 O PHE H 95
SHEET 5 AA2 6 GLU H 46 MET H 51 -1 O MET H 48 N TRP H 36
SHEET 6 AA2 6 VAL H 58 ASN H 59 -1 O ASN H 59 N TRP H 50
SHEET 1 AA3 4 GLN H 10 LYS H 13 0
SHEET 2 AA3 4 THR H 119 SER H 124 1 O THR H 122 N LYS H 12
SHEET 3 AA3 4 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 119
SHEET 4 AA3 4 HIS H 114 TRP H 115 -1 O HIS H 114 N ARG H 98
SHEET 1 AA4 2 TYR H 101 CYS H 102 0
SHEET 2 AA4 2 TYR H 107 TYR H 108 -1 O TYR H 108 N TYR H 101
SHEET 1 AA5 4 SER H 132 LEU H 136 0
SHEET 2 AA5 4 THR H 147 TYR H 157 -1 O LEU H 153 N PHE H 134
SHEET 3 AA5 4 TYR H 188 PRO H 197 -1 O LEU H 190 N VAL H 154
SHEET 4 AA5 4 VAL H 175 THR H 177 -1 N HIS H 176 O VAL H 193
SHEET 1 AA6 4 THR H 143 SER H 144 0
SHEET 2 AA6 4 THR H 147 TYR H 157 -1 O THR H 147 N SER H 144
SHEET 3 AA6 4 TYR H 188 PRO H 197 -1 O LEU H 190 N VAL H 154
SHEET 4 AA6 4 VAL H 181 LEU H 182 -1 N VAL H 181 O SER H 189
SHEET 1 AA7 3 THR H 163 TRP H 166 0
SHEET 2 AA7 3 TYR H 206 HIS H 212 -1 O ASN H 209 N SER H 165
SHEET 3 AA7 3 THR H 217 VAL H 223 -1 O THR H 217 N HIS H 212
SHEET 1 AA8 4 THR L 7 SER L 9 0
SHEET 2 AA8 4 ALA L 21 ARG L 26 -1 O ARG L 26 N THR L 7
SHEET 3 AA8 4 ASP L 70 ILE L 75 -1 O TYR L 71 N CYS L 25
SHEET 4 AA8 4 PHE L 62 SER L 67 -1 N THR L 63 O THR L 74
SHEET 1 AA9 6 THR L 12 SER L 14 0
SHEET 2 AA9 6 THR L 102 GLU L 105 1 O GLU L 105 N LEU L 13
SHEET 3 AA9 6 GLY L 84 GLN L 90 -1 N GLY L 84 O VAL L 104
SHEET 4 AA9 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87
SHEET 5 AA9 6 ARG L 45 TYR L 49 -1 O VAL L 47 N TRP L 35
SHEET 6 AA9 6 SER L 53 ARG L 54 -1 O SER L 53 N TYR L 49
SHEET 1 AB1 4 THR L 12 SER L 14 0
SHEET 2 AB1 4 THR L 102 GLU L 105 1 O GLU L 105 N LEU L 13
SHEET 3 AB1 4 GLY L 84 GLN L 90 -1 N GLY L 84 O VAL L 104
SHEET 4 AB1 4 PHE L 97 PHE L 98 -1 O PHE L 97 N GLN L 90
SHEET 1 AB2 4 SER L 116 PHE L 120 0
SHEET 2 AB2 4 THR L 131 PHE L 141 -1 O VAL L 135 N PHE L 120
SHEET 3 AB2 4 TYR L 175 SER L 184 -1 O LEU L 177 N LEU L 138
SHEET 4 AB2 4 SER L 161 VAL L 165 -1 N GLN L 162 O THR L 180
SHEET 1 AB3 4 ALA L 155 LEU L 156 0
SHEET 2 AB3 4 LYS L 147 VAL L 152 -1 N VAL L 152 O ALA L 155
SHEET 3 AB3 4 VAL L 193 THR L 199 -1 O GLU L 197 N GLN L 149
SHEET 4 AB3 4 VAL L 207 ASN L 212 -1 O VAL L 207 N VAL L 198
SHEET 1 AB4 5 LYS G 46 GLU G 47 0
SHEET 2 AB4 5 TYR G 487 LYS G 491 -1 O LYS G 491 N LYS G 46
SHEET 3 AB4 5 PHE G 223 CYS G 228 -1 N LEU G 226 O LYS G 488
SHEET 4 AB4 5 VAL G 242 VAL G 245 -1 O VAL G 245 N ILE G 225
SHEET 5 AB4 5 VAL G 84 LEU G 86 -1 N LEU G 86 O VAL G 242
SHEET 1 AB5 3 CYS G 74 PRO G 76 0
SHEET 2 AB5 3 PHE G 53 SER G 56 1 N CYS G 54 O VAL G 75
SHEET 3 AB5 3 HIS G 216 CYS G 218 -1 O CYS G 218 N PHE G 53
SHEET 1 AB6 2 GLU G 91 ASN G 94 0
SHEET 2 AB6 2 THR G 236 CYS G 239 -1 O GLY G 237 N PHE G 93
SHEET 1 AB7 4 SER G 199 THR G 202 0
SHEET 2 AB7 4 VAL G 120 THR G 123 -1 N LYS G 121 O ILE G 201
SHEET 3 AB7 4 LYS G 432 MET G 434 -1 O LYS G 432 N LEU G 122
SHEET 4 AB7 4 ILE G 423 ASN G 425 -1 N ILE G 424 O ALA G 433
SHEET 1 AB8 7 LEU G 259 LEU G 261 0
SHEET 2 AB8 7 ILE G 443 ARG G 456 -1 O GLY G 451 N LEU G 260
SHEET 3 AB8 7 ILE G 284 ARG G 298 -1 N VAL G 292 O ILE G 449
SHEET 4 AB8 7 GLN G 328 SER G 334 -1 O ASN G 332 N ASN G 295
SHEET 5 AB8 7 ASN G 413 LYS G 421 -1 O ILE G 414 N ILE G 333
SHEET 6 AB8 7 GLU G 381 CYS G 385 -1 N TYR G 384 O ARG G 419
SHEET 7 AB8 7 HIS G 374 CYS G 378 -1 N PHE G 376 O PHE G 383
SHEET 1 AB9 6 VAL G 271 ARG G 273 0
SHEET 2 AB9 6 ILE G 284 ARG G 298 -1 O ILE G 285 N ARG G 273
SHEET 3 AB9 6 ILE G 443 ARG G 456 -1 O ILE G 449 N VAL G 292
SHEET 4 AB9 6 THR G 466 PRO G 471 -1 O ARG G 470 N THR G 455
SHEET 5 AB9 6 THR G 358 PHE G 361 1 N ALA G 360 O GLU G 467
SHEET 6 AB9 6 SER G 393 TRP G 395 -1 O TRP G 395 N ILE G 359
SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.66
SSBOND 2 CYS H 32 CYS H 102 1555 1555 2.72
SSBOND 3 CYS L 25 CYS L 88 1555 1555 2.64
SSBOND 4 CYS L 136 CYS L 196 1555 1555 2.90
SSBOND 5 CYS G 54 CYS G 74 1555 1555 2.87
SSBOND 6 CYS G 119 CYS G 205 1555 1555 2.95
SSBOND 7 CYS G 228 CYS G 239 1555 1555 2.97
SSBOND 8 CYS G 378 CYS G 445 1555 1555 2.37
SSBOND 9 CYS G 385 CYS G 418 1555 1555 2.87
LINK ND2 ASN G 234 C1 NAG G 601 1555 1555 1.43
LINK ND2 ASN G 262 C1 NAG G 605 1555 1555 1.43
LINK ND2 ASN G 289 C1 NAG G 604 1555 1555 1.44
LINK ND2 ASN G 295 C1 NAG G 603 1555 1555 1.44
LINK ND2 ASN G 362 C1 NAG G 606 1555 1555 1.31
LINK ND2 ASN G 386 C1 NAG G 607 1555 1555 1.57
LINK ND2 ASN G 392 C1 NAG G 608 1555 1555 1.44
LINK ND2 ASN G 413 C1 NAG G 602 1555 1555 1.43
CISPEP 1 PHE H 158 PRO H 159 0 -5.30
CISPEP 2 GLU H 160 PRO H 161 0 4.15
CISPEP 3 SER L 9 PRO L 10 0 -3.98
CISPEP 4 TYR L 142 PRO L 143 0 -1.50
CRYST1 67.641 69.334 200.546 90.00 90.00 90.00 P 21 21 21 4
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 0.014784 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014423 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004986 0.00000