HEADER IMMUNE SYSTEM 07-NOV-11 3UJI TITLE CRYSTAL STRUCTURE OF ANTI-HIV-1 V3 FAB 2558 IN COMPLEX WITH MN PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF ANTI-HIV-1 V3 MONOCLONAL ANTIBODY 2558; COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: FAB REGION OF THE HEAVY CHAIN OF ANTI-HIV-1 V3 MONOCLONAL COMPND 6 ANTIBODY 2558; COMPND 7 CHAIN: H; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: ENVELOPE GLYCOPROTEIN GP160; COMPND 10 CHAIN: P; COMPND 11 FRAGMENT: UNP RESIDUES 306-328; COMPND 12 SYNONYM: ENV POLYPROTEIN, SURFACE PROTEIN GP120, SU, GLYCOPROTEIN COMPND 13 120, GP120, TRANSMEMBRANE PROTEIN GP41, TM, GLYCOPROTEIN 41, GP41; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 OTHER_DETAILS: IMMUNE SYSTEM; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_TAXID: 9606; SOURCE 8 OTHER_DETAILS: IMMUNE SYSTEM; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HIV-1 M:B_MN; SOURCE 12 ORGANISM_COMMON: HIV-1; SOURCE 13 ORGANISM_TAXID: 11696 KEYWDS IG DOMAINS, ANTIBODY FAB, ANTIGEN BINDING, THE THIRD VARIABLE REGION KEYWDS 2 OF HIV-1 GP120, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR X.P.KONG REVDAT 4 27-NOV-24 3UJI 1 HETSYN REVDAT 3 29-JUL-20 3UJI 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 08-NOV-17 3UJI 1 REMARK REVDAT 1 28-DEC-11 3UJI 0 JRNL AUTH M.K.GORNY,J.SAMPSON,H.LI,X.JIANG,M.TOTROV,X.H.WANG, JRNL AUTH 2 C.WILLIAMS,T.O'NEAL,B.VOLSKY,L.LI,T.CARDOZO,P.NYAMBI, JRNL AUTH 3 S.ZOLLA-PAZNER,X.P.KONG JRNL TITL HUMAN ANTI-V3 HIV-1 MONOCLONAL ANTIBODIES ENCODED BY THE JRNL TITL 2 VH5-51/VL LAMBDA GENES DEFINE A CONSERVED ANTIGENIC JRNL TITL 3 STRUCTURE. JRNL REF PLOS ONE V. 6 27780 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 22164215 JRNL DOI 10.1371/JOURNAL.PONE.0027780 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 68884 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3662 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4943 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 247 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3358 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 716 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.28000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.362 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3491 ; 0.028 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4762 ; 2.633 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 440 ; 7.251 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;33.998 ;24.646 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 533 ;11.898 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;14.034 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 536 ; 0.215 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2608 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3UJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068833. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97854 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43100 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85MM HEPES-NA, 15% GLYCEROL, 17% PEG REMARK 280 4K, 8.5% ISOPROPANOL, PH 7.5, EVAPORATION, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 51.17550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.54850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.17550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.54850 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: 6380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, P, 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 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 SER L 1 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 LYS P 321 REMARK 465 ASN P 322 REMARK 465 ILE P 323 REMARK 465 ILE P 324 REMARK 465 GLY P 325 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 HOH L 390 O HOH H 632 1.80 REMARK 500 O HOH L 301 O HOH L 416 1.89 REMARK 500 O HOH L 360 O HOH L 373 2.00 REMARK 500 O HOH L 439 O HOH H 579 2.08 REMARK 500 O HOH H 336 O HOH H 680 2.09 REMARK 500 O HOH H 494 O HOH H 531 2.10 REMARK 500 O HOH H 288 O HOH H 711 2.12 REMARK 500 O HOH L 252 O HOH L 715 2.12 REMARK 500 O HOH L 412 O HOH L 620 2.13 REMARK 500 O HOH H 675 O HOH H 677 2.14 REMARK 500 OE1 GLU L 203 O HOH L 308 2.16 REMARK 500 O HOH H 596 O HOH H 677 2.17 REMARK 500 O HOH H 551 O HOH H 685 2.17 REMARK 500 O HOH L 584 O HOH L 608 2.17 REMARK 500 O HOH L 402 O HOH L 556 2.17 REMARK 500 O HOH H 370 O HOH H 521 2.18 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 O HOH L 296 O HOH L 405 3545 1.75 REMARK 500 O HOH L 350 O HOH L 373 3545 1.94 REMARK 500 O HOH H 409 O HOH P 255 4445 1.95 REMARK 500 O HOH L 313 O HOH L 336 4556 2.08 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 GLU L 50 CD GLU L 50 OE1 0.067 REMARK 500 ARG L 61 CZ ARG L 61 NH1 0.095 REMARK 500 TRP H 82 CE2 TRP H 82 CD2 0.078 REMARK 500 HIS H 164 CA HIS H 164 CB -0.139 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 ASP L 51 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG L 61 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG L 61 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 ASP L 82 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES REMARK 500 GLU L 124 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 LEU L 180 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG H 94 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP H 101 CB - CG - OD2 ANGL. DEV. = -6.2 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 L 51 -48.35 73.37 REMARK 500 ASP L 151 -112.04 52.69 REMARK 500 GLN H 64 137.54 -38.03 REMARK 500 ALA H 88 170.42 179.06 REMARK 500 ASP H 144 64.43 62.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UJJ RELATED DB: PDB DBREF 3UJI P 301 325 UNP P05877 ENV_HV1MN 306 328 DBREF 3UJI L 1 208 PDB 3UJI 3UJI 1 208 DBREF 3UJI H 1 213 PDB 3UJI 3UJI 1 213 SEQRES 1 L 209 SER TYR GLU LEU THR GLN PRO PRO SER VAL SER VAL SER SEQRES 2 L 209 PRO GLY GLN THR ALA SER ILE THR CYS SER GLY ASP ILE SEQRES 3 L 209 LEU GLY ASP LYS TYR VAL SER TRP TYR GLN GLN LYS SER SEQRES 4 L 209 GLY GLN SER PRO LEU LEU VAL ILE TYR GLU ASP THR LYS SEQRES 5 L 209 ARG PRO SER GLY ILE PRO ASP ARG PHE SER GLY SER LYS SEQRES 6 L 209 SER GLY ASN THR ALA THR LEU THR ILE SER GLY THR GLN SEQRES 7 L 209 ALA MET ASP GLU ALA ASP TYR TYR CYS GLN ALA TRP ASP SEQRES 8 L 209 SER THR LEU GLY VAL VAL PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 209 THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SER VAL THR SEQRES 10 L 209 LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA ASN LYS SEQRES 11 L 209 ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR PRO GLY SEQRES 12 L 209 ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER PRO VAL SEQRES 13 L 209 LYS ALA GLY VAL GLU THR THR THR PRO SER LYS GLN SER SEQRES 14 L 209 ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER LEU THR SEQRES 15 L 209 PRO GLU GLN TRP LYS SER HIS LYS SER TYR SER CYS GLN SEQRES 16 L 209 VAL THR HIS GLU GLY SER THR VAL GLU LYS THR VAL ALA SEQRES 17 L 209 PRO SEQRES 1 H 223 GLN VAL GLN LEU VAL GLN SER ALA ALA GLU VAL LYS LYS SEQRES 2 H 223 PRO GLY GLU ALA LEU LYS ILE SER CYS LYS GLY SER GLY SEQRES 3 H 223 TYR SER PHE SER ASN TYR TRP ILE ALA TRP VAL ARG GLN SEQRES 4 H 223 MET PRO GLY LYS GLY LEU GLU TRP MET GLY ILE VAL TYR SEQRES 5 H 223 PRO ASP ASP SER ASP SER SER TYR ASN SER SER PHE GLN SEQRES 6 H 223 GLY GLN ILE THR PHE SER ALA ASP LYS SER ILE SER THR SEQRES 7 H 223 ALA TYR LEU HIS TRP THR SER LEU GLN ALA SER ASP THR SEQRES 8 H 223 ALA MET TYR TYR CYS ALA ARG LEU GLY PHE GLU GLY ASP SEQRES 9 H 223 TYR SER GLY SER PHE PHE ASP TYR TRP GLY GLN GLY THR SEQRES 10 H 223 LEU LEU ILE VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 223 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 223 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 223 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 223 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 223 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 223 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 223 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 223 GLU PRO SEQRES 1 P 23 TYR ASN LYS ARG LYS ARG ILE HIS ILE GLY PRO GLY ARG SEQRES 2 P 23 ALA PHE TYR THR THR LYS ASN ILE ILE GLY MODRES 3UJI ASN H 60 ASN GLYCOSYLATION SITE HET NAG A 1 14 HET NAG A 2 14 HET FUC A 3 10 HET CA L 209 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CA CALCIUM ION 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 HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 FUC C6 H12 O5 FORMUL 5 CA CA 2+ FORMUL 6 HOH *716(H2 O) HELIX 1 2 ASP L 26 LYS L 31 5 6 HELIX 2 3 GLN L 79 GLU L 83 5 5 HELIX 3 4 SER L 121 ALA L 127 1 7 HELIX 4 5 THR L 181 SER L 187 1 7 HELIX 5 6 SER H 28 TYR H 32 5 5 HELIX 6 7 LYS H 73 ILE H 75 5 3 HELIX 7 8 GLN H 83 THR H 87 5 5 HELIX 8 9 SER H 156 ALA H 158 5 3 HELIX 9 10 SER H 187 THR H 191 5 5 HELIX 10 11 LYS H 201 ASN H 204 5 4 HELIX 11 1 ASN P 302 ARG P 306 5 5 SHEET 1 A 2 HIS P 308 GLY P 312 0 SHEET 2 A 2 ALA P 316 PHE P 317 -1 O ALA P 316 N ILE P 309 SHEET 1 B 5 SER L 9 VAL L 13 0 SHEET 2 B 5 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 11 SHEET 3 B 5 ALA L 84 ASP L 92 -1 N ALA L 84 O VAL L 104 SHEET 4 B 5 SER L 34 GLN L 38 -1 N GLN L 38 O ASP L 85 SHEET 5 B 5 LEU L 45 ILE L 48 -1 O VAL L 47 N TRP L 35 SHEET 1 C 4 SER L 9 VAL L 13 0 SHEET 2 C 4 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 11 SHEET 3 C 4 ALA L 84 ASP L 92 -1 N ALA L 84 O VAL L 104 SHEET 4 C 4 GLY L 95A PHE L 98 -1 O GLY L 95A N ASP L 92 SHEET 1 D 3 ALA L 19 SER L 24 0 SHEET 2 D 3 THR L 70 ILE L 75 -1 O ILE L 75 N ALA L 19 SHEET 3 D 3 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 E 4 SER L 114 PHE L 118 0 SHEET 2 E 4 ALA L 130 PHE L 139 -1 O SER L 137 N SER L 114 SHEET 3 E 4 TYR L 172 LEU L 180 -1 O LEU L 178 N LEU L 132 SHEET 4 E 4 VAL L 159 THR L 161 -1 N GLU L 160 O TYR L 177 SHEET 1 F 4 SER L 114 PHE L 118 0 SHEET 2 F 4 ALA L 130 PHE L 139 -1 O SER L 137 N SER L 114 SHEET 3 F 4 TYR L 172 LEU L 180 -1 O LEU L 178 N LEU L 132 SHEET 4 F 4 SER L 165 LYS L 166 -1 N SER L 165 O ALA L 173 SHEET 1 G 4 SER L 153 VAL L 155 0 SHEET 2 G 4 THR L 145 ALA L 150 -1 N ALA L 150 O SER L 153 SHEET 3 G 4 TYR L 191 HIS L 197 -1 O GLN L 194 N ALA L 147 SHEET 4 G 4 SER L 200 VAL L 206 -1 O SER L 200 N HIS L 197 SHEET 1 H 4 GLN H 3 GLN H 6 0 SHEET 2 H 4 LEU H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 H 4 THR H 77 TRP H 82 -1 O TRP H 82 N LEU H 18 SHEET 4 H 4 ILE H 67 ASP H 72 -1 N THR H 68 O HIS H 81 SHEET 1 I 6 GLU H 10 LYS H 12 0 SHEET 2 I 6 THR H 107 VAL H 111 1 O ILE H 110 N GLU H 10 SHEET 3 I 6 ALA H 88 GLU H 98 -1 N ALA H 88 O LEU H 109 SHEET 4 I 6 ILE H 34 GLN H 39 -1 N ALA H 35 O ALA H 93 SHEET 5 I 6 GLU H 46 VAL H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 I 6 SER H 57 TYR H 59 -1 O SER H 58 N ILE H 50 SHEET 1 J 4 GLU H 10 LYS H 12 0 SHEET 2 J 4 THR H 107 VAL H 111 1 O ILE H 110 N GLU H 10 SHEET 3 J 4 ALA H 88 GLU H 98 -1 N ALA H 88 O LEU H 109 SHEET 4 J 4 TYR H 100A TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 K 4 SER H 120 LEU H 124 0 SHEET 2 K 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 K 4 TYR H 176 PRO H 185 -1 O VAL H 184 N ALA H 136 SHEET 4 K 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 L 4 SER H 120 LEU H 124 0 SHEET 2 L 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 L 4 TYR H 176 PRO H 185 -1 O VAL H 184 N ALA H 136 SHEET 4 L 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 M 3 THR H 151 TRP H 154 0 SHEET 2 M 3 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 M 3 THR H 205 VAL H 211 -1 O VAL H 207 N VAL H 198 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.10 SSBOND 2 CYS L 134 CYS L 193 1555 1555 2.07 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.13 SSBOND 4 CYS H 140 CYS H 196 1555 1555 2.05 LINK ND2 ASN H 60 C1 NAG A 1 1555 1555 1.42 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.40 LINK O6 NAG A 1 C1 FUC A 3 1555 1555 1.49 LINK CA CA L 209 O HOH L 210 1555 1555 3.12 CISPEP 1 TYR L 140 PRO L 141 0 -3.55 CISPEP 2 GLY H 133 GLY H 134 0 6.77 CISPEP 3 PHE H 146 PRO H 147 0 -4.43 CISPEP 4 GLU H 148 PRO H 149 0 6.07 CRYST1 102.351 73.097 88.662 90.00 121.98 90.00 C 1 2 1 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 0.009770 0.000000 0.006100 0.00000 SCALE2 0.000000 0.013680 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013297 0.00000