HEADER VIRAL PROTEIN/IMMUNE SYSTEM 28-JAN-15 4XVT TITLE CRYSTAL STRUCTURE OF HIV-1 93TH057 COREE GP120 WITH ANTIBODY 45- TITLE 2 VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DONOR 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 COMPND 7 (VRC07_1995) HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 COMPND 12 (VRC07_1995) LIGHT CHAIN; COMPND 13 CHAIN: L; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; 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: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 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 4 23-OCT-24 4XVT 1 REMARK REVDAT 3 27-SEP-23 4XVT 1 HETSYN REVDAT 2 29-JUL-20 4XVT 1 COMPND SOURCE REMARK HETNAM REVDAT 2 2 1 LINK SITE REVDAT 1 15-JUL-15 4XVT 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. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 97823 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4882 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.1126 - 5.2459 0.99 3346 168 0.1808 0.2115 REMARK 3 2 5.2459 - 4.1662 1.00 3281 144 0.1387 0.1610 REMARK 3 3 4.1662 - 3.6403 1.00 3183 185 0.1523 0.1843 REMARK 3 4 3.6403 - 3.3077 1.00 3171 188 0.1631 0.1992 REMARK 3 5 3.3077 - 3.0708 1.00 3147 163 0.1790 0.2118 REMARK 3 6 3.0708 - 2.8899 1.00 3187 156 0.1877 0.2118 REMARK 3 7 2.8899 - 2.7452 1.00 3130 172 0.1927 0.2823 REMARK 3 8 2.7452 - 2.6257 1.00 3117 178 0.1948 0.2462 REMARK 3 9 2.6257 - 2.5247 1.00 3120 170 0.1981 0.2430 REMARK 3 10 2.5247 - 2.4376 1.00 3134 169 0.2005 0.2633 REMARK 3 11 2.4376 - 2.3614 1.00 3127 173 0.1973 0.2450 REMARK 3 12 2.3614 - 2.2939 1.00 3094 184 0.1940 0.2727 REMARK 3 13 2.2939 - 2.2335 1.00 3112 156 0.1944 0.2206 REMARK 3 14 2.2335 - 2.1791 1.00 3074 183 0.1927 0.2556 REMARK 3 15 2.1791 - 2.1295 1.00 3150 153 0.1917 0.2425 REMARK 3 16 2.1295 - 2.0842 1.00 3113 148 0.2011 0.2495 REMARK 3 17 2.0842 - 2.0425 1.00 3122 160 0.2073 0.2612 REMARK 3 18 2.0425 - 2.0040 1.00 3122 143 0.2104 0.2518 REMARK 3 19 2.0040 - 1.9682 1.00 3115 171 0.2060 0.2657 REMARK 3 20 1.9682 - 1.9348 1.00 3133 144 0.2059 0.2727 REMARK 3 21 1.9348 - 1.9036 1.00 3061 159 0.2205 0.3025 REMARK 3 22 1.9036 - 1.8743 1.00 3105 168 0.2300 0.2626 REMARK 3 23 1.8743 - 1.8468 1.00 3094 157 0.2429 0.2992 REMARK 3 24 1.8468 - 1.8208 1.00 3121 171 0.2446 0.2927 REMARK 3 25 1.8208 - 1.7962 1.00 3049 166 0.2477 0.2953 REMARK 3 26 1.7962 - 1.7728 1.00 3103 167 0.2569 0.2978 REMARK 3 27 1.7728 - 1.7507 1.00 3077 156 0.2667 0.2894 REMARK 3 28 1.7507 - 1.7296 1.00 3109 165 0.2699 0.3211 REMARK 3 29 1.7296 - 1.7095 1.00 3043 159 0.2914 0.3981 REMARK 3 30 1.7095 - 1.6903 0.70 2201 106 0.3046 0.3035 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.017 6354 REMARK 3 ANGLE : 1.823 8632 REMARK 3 CHIRALITY : 0.096 985 REMARK 3 PLANARITY : 0.010 1108 REMARK 3 DIHEDRAL : 15.364 2306 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -36.6069 -12.8401 -22.9555 REMARK 3 T TENSOR REMARK 3 T11: 0.2196 T22: 0.2257 REMARK 3 T33: 0.2524 T12: 0.0118 REMARK 3 T13: -0.0146 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.3604 L22: 0.8686 REMARK 3 L33: 1.4675 L12: 0.2561 REMARK 3 L13: 0.4312 L23: 0.9560 REMARK 3 S TENSOR REMARK 3 S11: -0.0333 S12: -0.0118 S13: 0.0304 REMARK 3 S21: -0.0517 S22: -0.0982 S23: 0.1103 REMARK 3 S31: -0.0877 S32: -0.1206 S33: 0.1196 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4XVT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 97827 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 34.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.080 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: 3NGB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA CACODYLATE PH 6.5, 12% PEG REMARK 280 8000, 0.16 M NAACETATE., 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 32.32350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 99.60950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.92050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 99.60950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.32350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.92050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, L 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 ASN G 404 REMARK 465 GLU G 405 REMARK 465 THR G 406 REMARK 465 MET G 407 REMARK 465 LYS G 408 REMARK 465 GLY G 409 REMARK 465 GLU L 3 REMARK 465 ILE L 4 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 ND2 ASN G 392 O5 NAG G 510 1.52 REMARK 500 CG ASN G 392 C1 NAG G 510 2.12 REMARK 500 ND2 ASN G 276 C2 NAG G 501 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 CYS H 102 CB CYS H 102 SG 0.122 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 H 19 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG H 19 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG H 38 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG H 38 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 MET H 51 CG - SD - CE ANGL. DEV. = -20.5 DEGREES REMARK 500 CYS H 102 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 LEU H 190 CA - CB - CG ANGL. DEV. = 19.0 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 ASP G 211 107.68 -161.07 REMARK 500 GLN G 258 -57.92 70.52 REMARK 500 GLU G 268 -96.97 -115.98 REMARK 500 ASN G 276 106.93 -170.98 REMARK 500 ASP G 325 108.91 -162.79 REMARK 500 ASN G 354 -130.97 59.14 REMARK 500 PRO G 437 155.24 -49.83 REMARK 500 ALA G 460 51.45 -97.21 REMARK 500 ASN G 462 -70.29 -67.15 REMARK 500 TYR L 91 -131.47 49.39 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 ASN G 354 ASN G 355 141.86 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 G 840 DISTANCE = 10.97 ANGSTROMS REMARK 525 HOH H 502 DISTANCE = 8.85 ANGSTROMS REMARK 525 HOH H 503 DISTANCE = 12.18 ANGSTROMS REMARK 525 HOH L 481 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH L 482 DISTANCE = 7.91 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XVS RELATED DB: PDB DBREF 4XVT G 44 492 PDB 4XVT 4XVT 44 492 DBREF 4XVT H 1 228 PDB 4XVT 4XVT 1 228 DBREF 4XVT L 3 216 PDB 4XVT 4XVT 3 216 SEQRES 1 G 353 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 G 353 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 G 353 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 G 353 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 G 353 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 G 353 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 G 353 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 G 353 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 G 353 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 G 353 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 G 353 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 G 353 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 G 353 ARG SER GLU ASN LEU THR ASN ASN ALA LYS THR ILE ILE SEQRES 14 G 353 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 G 353 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 G 353 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 G 353 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 G 353 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 G 353 ASP LEU GLU ILE THR MET HIS HIS PHE ASN CYS ARG GLY SEQRES 20 G 353 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 G 353 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 G 353 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 G 353 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 G 353 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 G 353 ILE LEU LEU THR ARG ASP GLY GLY ALA ASN ASN THR SER SEQRES 26 G 353 ASN GLU THR PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP SEQRES 27 G 353 ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN SEQRES 28 G 353 ILE GLU 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 HET NAG G 501 14 HET NAG G 502 14 HET NAG G 503 14 HET NAG G 504 14 HET NAG G 505 14 HET NAG G 506 14 HET NAG G 507 14 HET NAG G 508 14 HET NAG G 509 14 HET NAG G 510 14 HET NAG G 511 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 11(C8 H15 N O6) FORMUL 15 HOH *625(H2 O) HELIX 1 AA1 GLU G 64 ALA G 73 1 10 HELIX 2 AA2 ASN G 98 LEU G 116 1 19 HELIX 3 AA3 GLY G 335 PHE G 353 1 19 HELIX 4 AA4 ASP G 368 MET G 373 1 6 HELIX 5 AA5 THR G 387 PHE G 391 5 5 HELIX 6 AA6 ASN G 392 GLY G 397 5 6 HELIX 7 AA7 ASN G 474 TYR G 484 1 11 HELIX 8 AA8 THR H 28 CYS H 32 5 5 HELIX 9 AA9 PRO H 61 GLN H 65 5 5 HELIX 10 AB1 MET H 74 THR H 76 5 3 HELIX 11 AB2 ARG H 87 THR H 91 5 5 HELIX 12 AB3 SER H 139 LYS H 141 5 3 HELIX 13 AB4 SER H 168 ALA H 170 5 3 HELIX 14 AB5 SER H 199 THR H 203 5 5 HELIX 15 AB6 LYS H 213 ASN H 216 5 4 HELIX 16 AB7 GLU L 79 PHE L 83 5 5 HELIX 17 AB8 SER L 123 SER L 129 1 7 HELIX 18 AB9 LYS L 185 GLU L 189 1 5 SHEET 1 AA1 5 TRP G 45 ASP G 47 0 SHEET 2 AA1 5 TYR G 486 ILE G 491 -1 O GLN G 490 N LYS G 46 SHEET 3 AA1 5 TYR G 223 CYS G 228 -1 N LEU G 226 O LYS G 487 SHEET 4 AA1 5 VAL G 242 VAL G 245 -1 O SER G 243 N LYS G 227 SHEET 5 AA1 5 GLU G 83 LEU G 86 -1 N LEU G 86 O VAL G 242 SHEET 1 AA2 3 CYS G 74 PRO G 76 0 SHEET 2 AA2 3 PHE G 53 SER G 56 1 N CYS G 54 O VAL G 75 SHEET 3 AA2 3 ILE G 215 CYS G 218 -1 O HIS G 216 N ALA G 55 SHEET 1 AA3 2 GLU G 91 ASN G 94 0 SHEET 2 AA3 2 THR G 236 CYS G 239 -1 O GLY G 237 N PHE G 93 SHEET 1 AA4 4 VAL G 200 LYS G 202 0 SHEET 2 AA4 4 VAL G 120 LEU G 122 -1 N LYS G 121 O ILE G 201 SHEET 3 AA4 4 GLN G 432 MET G 434 -1 O MET G 434 N VAL G 120 SHEET 4 AA4 4 ILE G 423 ASN G 425 -1 N ILE G 424 O ALA G 433 SHEET 1 AA5 5 LEU G 259 LEU G 261 0 SHEET 2 AA5 5 ILE G 443 ARG G 456 -1 O THR G 450 N LEU G 260 SHEET 3 AA5 5 ILE G 284 ARG G 298 -1 N VAL G 286 O ILE G 452 SHEET 4 AA5 5 ASN G 465 PRO G 470 0 SHEET 5 AA5 5 THR G 358 PHE G 361 1 N THR G 358 O GLU G 466 SHEET 1 AA6 7 ILE G 271 ARG G 273 0 SHEET 2 AA6 7 ILE G 284 ARG G 298 -1 O HIS G 287 N ILE G 271 SHEET 3 AA6 7 ILE G 443 ARG G 456 -1 O ILE G 452 N VAL G 286 SHEET 4 AA6 7 LYS G 328 ASN G 334 0 SHEET 5 AA6 7 THR G 413 LYS G 421 -1 O ILE G 414 N ILE G 333 SHEET 6 AA6 7 GLU G 381 CYS G 385 -1 N PHE G 382 O LYS G 421 SHEET 7 AA6 7 HIS G 374 CYS G 378 -1 N HIS G 374 O CYS G 385 SHEET 1 AA7 4 GLN H 3 GLN H 6 0 SHEET 2 AA7 4 MET H 18 SER H 25 -1 O LYS H 23 N LEU H 5 SHEET 3 AA7 4 THR H 78 MET H 83 -1 O MET H 83 N MET H 18 SHEET 4 AA7 4 VAL H 68 ASP H 73 -1 N ASP H 73 O THR H 78 SHEET 1 AA8 6 GLN H 10 LYS H 12 0 SHEET 2 AA8 6 THR H 119 VAL H 123 1 O THR H 122 N LYS H 12 SHEET 3 AA8 6 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 119 SHEET 4 AA8 6 ILE H 34 GLN H 39 -1 N VAL H 37 O PHE H 95 SHEET 5 AA8 6 LEU H 45 LYS H 52 -1 O MET H 48 N TRP H 36 SHEET 6 AA8 6 ALA H 57 ASN H 59 -1 O ALA H 57 N LYS H 52 SHEET 1 AA9 4 GLN H 10 LYS H 12 0 SHEET 2 AA9 4 THR H 119 VAL H 123 1 O THR H 122 N LYS H 12 SHEET 3 AA9 4 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 119 SHEET 4 AA9 4 HIS H 114 TRP H 115 -1 O HIS H 114 N ARG H 98 SHEET 1 AB1 2 TYR H 101 CYS H 102 0 SHEET 2 AB1 2 TYR H 107 TYR H 108 -1 O TYR H 108 N TYR H 101 SHEET 1 AB2 4 SER H 132 LEU H 136 0 SHEET 2 AB2 4 THR H 147 TYR H 157 -1 O LEU H 153 N PHE H 134 SHEET 3 AB2 4 TYR H 188 PRO H 197 -1 O LEU H 190 N VAL H 154 SHEET 4 AB2 4 VAL H 175 THR H 177 -1 N HIS H 176 O VAL H 193 SHEET 1 AB3 4 THR H 143 SER H 144 0 SHEET 2 AB3 4 THR H 147 TYR H 157 -1 O THR H 147 N SER H 144 SHEET 3 AB3 4 TYR H 188 PRO H 197 -1 O LEU H 190 N VAL H 154 SHEET 4 AB3 4 VAL H 181 LEU H 182 -1 N VAL H 181 O SER H 189 SHEET 1 AB4 3 THR H 163 TRP H 166 0 SHEET 2 AB4 3 ILE H 207 HIS H 212 -1 O ASN H 209 N SER H 165 SHEET 3 AB4 3 THR H 217 LYS H 222 -1 O THR H 217 N HIS H 212 SHEET 1 AB5 4 LEU L 6 SER L 9 0 SHEET 2 AB5 4 ALA L 21 THR L 27 -1 O ARG L 26 N THR L 7 SHEET 3 AB5 4 ASP L 70 ILE L 75 -1 O LEU L 73 N LEU L 23 SHEET 4 AB5 4 PHE L 62 SER L 67 -1 N SER L 67 O ASP L 70 SHEET 1 AB6 6 THR L 12 SER L 14 0 SHEET 2 AB6 6 THR L 102 GLU L 105 1 O GLU L 105 N LEU L 13 SHEET 3 AB6 6 GLY L 84 GLN L 90 -1 N GLY L 84 O VAL L 104 SHEET 4 AB6 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 AB6 6 ARG L 45 TYR L 49 -1 O VAL L 47 N TRP L 35 SHEET 6 AB6 6 SER L 53 ARG L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AB7 4 THR L 12 SER L 14 0 SHEET 2 AB7 4 THR L 102 GLU L 105 1 O GLU L 105 N LEU L 13 SHEET 3 AB7 4 GLY L 84 GLN L 90 -1 N GLY L 84 O VAL L 104 SHEET 4 AB7 4 PHE L 97 PHE L 98 -1 O PHE L 97 N GLN L 90 SHEET 1 AB8 4 SER L 116 PHE L 120 0 SHEET 2 AB8 4 THR L 131 PHE L 141 -1 O ASN L 139 N SER L 116 SHEET 3 AB8 4 TYR L 175 SER L 184 -1 O LEU L 183 N ALA L 132 SHEET 4 AB8 4 SER L 161 VAL L 165 -1 N GLN L 162 O THR L 180 SHEET 1 AB9 4 ALA L 155 LEU L 156 0 SHEET 2 AB9 4 LYS L 147 VAL L 152 -1 N VAL L 152 O ALA L 155 SHEET 3 AB9 4 VAL L 193 THR L 199 -1 O ALA L 195 N LYS L 151 SHEET 4 AB9 4 VAL L 207 ASN L 212 -1 O VAL L 207 N VAL L 198 SSBOND 1 CYS G 54 CYS G 74 1555 1555 2.13 SSBOND 2 CYS G 119 CYS G 205 1555 1555 2.06 SSBOND 3 CYS G 218 CYS G 247 1555 1555 2.15 SSBOND 4 CYS G 228 CYS G 239 1555 1555 2.11 SSBOND 5 CYS G 296 CYS G 331 1555 1555 2.09 SSBOND 6 CYS G 378 CYS G 445 1555 1555 2.06 SSBOND 7 CYS G 385 CYS G 418 1555 1555 2.03 SSBOND 8 CYS G 395 CYS G 410 1555 1555 2.63 SSBOND 9 CYS H 22 CYS H 96 1555 1555 2.10 SSBOND 10 CYS H 32 CYS H 102 1555 1555 2.12 SSBOND 11 CYS H 152 CYS H 208 1555 1555 2.03 SSBOND 12 CYS L 25 CYS L 88 1555 1555 2.16 SSBOND 13 CYS L 136 CYS L 196 1555 1555 2.07 LINK ND2 ASN G 88 C1 NAG G 503 1555 1555 1.45 LINK ND2 ASN G 234 C1 NAG G 502 1555 1555 1.43 LINK ND2 ASN G 241 C1 NAG G 504 1555 1555 1.45 LINK ND2 ASN G 262 C1 NAG G 506 1555 1555 1.43 LINK ND2 ASN G 276 C1 NAG G 501 1555 1555 1.40 LINK ND2 ASN G 289 C1 NAG G 505 1555 1555 1.44 LINK ND2 ASN G 295 C1 NAG G 507 1555 1555 1.44 LINK ND2 ASN G 334 C1 NAG G 508 1555 1555 1.41 LINK ND2 ASN G 386 C1 NAG G 509 1555 1555 1.45 LINK ND2 ASN G 392 C1 NAG G 510 1555 1555 1.42 LINK ND2 ASN G 461 C1 NAG G 511 1555 1555 1.43 CISPEP 1 GLY G 124 GLY G 198 0 1.34 CISPEP 2 PHE H 158 PRO H 159 0 -3.49 CISPEP 3 GLU H 160 PRO H 161 0 -0.27 CISPEP 4 SER L 9 PRO L 10 0 -6.14 CISPEP 5 TYR L 142 PRO L 143 0 3.57 CRYST1 64.647 67.841 199.219 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 0.015469 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014740 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005020 0.00000