HEADER IMMUNE SYSTEM 14-SEP-05 2B0S TITLE CRYSTAL STRUCTURE ANALYSIS OF ANTI-HIV-1 V3 FAB 2219 IN COMPLEX WITH TITLE 2 MN PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB 2219, LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: LIGHT CHAIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB 2219, HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 FRAGMENT: HEAVY CHAIN; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: MN PEPTIDE OF EXTERIOR MEMBRANE GLYCOPROTEIN GP120; COMPND 11 CHAIN: P; COMPND 12 FRAGMENT: RESIDUES 308-325; COMPND 13 SYNONYM: GP120; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BLOOD; SOURCE 6 CELL: PERIPHERAL BLOOD CELLS; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 ORGAN: BLOOD; SOURCE 12 CELL: PERIPHERAL BLOOD CELLS; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: THIS SEQUENCE OCCURS IN HUMAN IMMUNODEFICIENCY VIRUS SOURCE 16 TYPE 1 (ISOLATE MN) KEYWDS FAB-PEPTIDE COMPLEX; HIV-1; GP120; V3 LOOP, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.L.STANFIELD,M.K.GORNY,S.ZOLLA-PAZNER,I.A.WILSON REVDAT 5 23-AUG-23 2B0S 1 REMARK SEQADV REVDAT 4 24-JUL-19 2B0S 1 REMARK REVDAT 3 13-JUL-11 2B0S 1 VERSN REVDAT 2 24-FEB-09 2B0S 1 VERSN REVDAT 1 04-JUL-06 2B0S 0 JRNL AUTH R.L.STANFIELD,M.K.GORNY,S.ZOLLA-PAZNER,I.A.WILSON JRNL TITL CRYSTAL STRUCTURES OF HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 JRNL TITL 2 (HIV-1) NEUTRALIZING ANTIBODY 2219 IN COMPLEX WITH THREE JRNL TITL 3 DIFFERENT V3 PEPTIDES REVEAL A NEW BINDING MODE FOR HIV-1 JRNL TITL 4 CROSS-REACTIVITY. JRNL REF J.VIROL. V. 80 6093 2006 JRNL REFN ISSN 0022-538X JRNL PMID 16731948 JRNL DOI 10.1128/JVI.00205-06 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22624 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1195 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1643 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3449 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 191 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 30.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -1.89000 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): 0.344 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.251 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.271 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3558 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3066 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4840 ; 1.458 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7199 ; 0.920 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 453 ; 7.231 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;33.716 ;24.104 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 545 ;13.882 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;12.049 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 528 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3968 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 694 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 550 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3029 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1651 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2127 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 224 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.144 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 27 ; 0.241 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.169 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2884 ; 0.751 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 929 ; 0.127 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3670 ; 0.937 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1553 ; 1.494 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1170 ; 2.133 ; 4.500 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 107 REMARK 3 ORIGIN FOR THE GROUP (A): 24.5841 61.8127 144.2352 REMARK 3 T TENSOR REMARK 3 T11: -0.0068 T22: -0.1347 REMARK 3 T33: -0.1246 T12: 0.0135 REMARK 3 T13: 0.0421 T23: 0.0385 REMARK 3 L TENSOR REMARK 3 L11: 6.1882 L22: 0.7634 REMARK 3 L33: 1.7484 L12: -0.7633 REMARK 3 L13: 0.1015 L23: -0.5957 REMARK 3 S TENSOR REMARK 3 S11: 0.0182 S12: 0.5743 S13: 0.0324 REMARK 3 S21: -0.3117 S22: -0.0874 S23: -0.2625 REMARK 3 S31: 0.1148 S32: 0.0255 S33: 0.0692 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 108 L 212 REMARK 3 ORIGIN FOR THE GROUP (A): 43.3703 37.9077 151.6725 REMARK 3 T TENSOR REMARK 3 T11: -0.0179 T22: -0.0657 REMARK 3 T33: -0.0424 T12: -0.0304 REMARK 3 T13: -0.0090 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.9080 L22: 5.9426 REMARK 3 L33: 4.7809 L12: -0.4362 REMARK 3 L13: -0.0835 L23: -3.1832 REMARK 3 S TENSOR REMARK 3 S11: 0.1341 S12: 0.2237 S13: -0.2653 REMARK 3 S21: -0.1342 S22: -0.0333 S23: 0.0368 REMARK 3 S31: 0.5044 S32: -0.3384 S33: -0.1009 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 113 REMARK 3 RESIDUE RANGE : P 303 P 320 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3402 59.2174 161.8069 REMARK 3 T TENSOR REMARK 3 T11: -0.0829 T22: -0.2365 REMARK 3 T33: -0.1497 T12: -0.0104 REMARK 3 T13: 0.0160 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 1.4146 L22: 1.8712 REMARK 3 L33: 2.7912 L12: -0.4927 REMARK 3 L13: 0.6642 L23: -1.2591 REMARK 3 S TENSOR REMARK 3 S11: 0.0271 S12: 0.0205 S13: -0.0227 REMARK 3 S21: 0.0674 S22: 0.0007 S23: 0.0808 REMARK 3 S31: -0.0228 S32: -0.1118 S33: -0.0279 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 114 H 229 REMARK 3 ORIGIN FOR THE GROUP (A): 52.8271 38.7713 165.0012 REMARK 3 T TENSOR REMARK 3 T11: 0.0354 T22: -0.1607 REMARK 3 T33: -0.0504 T12: -0.0034 REMARK 3 T13: -0.0402 T23: 0.0304 REMARK 3 L TENSOR REMARK 3 L11: 7.8389 L22: 2.3965 REMARK 3 L33: 2.4069 L12: 0.0011 REMARK 3 L13: -1.1181 L23: -1.2101 REMARK 3 S TENSOR REMARK 3 S11: -0.0301 S12: 0.1349 S13: -0.2679 REMARK 3 S21: -0.0692 S22: -0.0086 S23: -0.2177 REMARK 3 S31: 0.2718 S32: -0.0225 S33: 0.0387 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2B0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23835 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 69.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.52500 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 7FAB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 400, 0.2M POTASSIUM ACETATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 137.59700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.23550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.23550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.79850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.23550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.23550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 206.39550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.23550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.23550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.79850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.23550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.23550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 206.39550 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 137.59700 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: 5550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, P 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 LYS P 321 REMARK 465 ASN P 322 REMARK 465 ALA P 323 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER H 229 O 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 OD1 ASN L 31 NH2 ARG P 315 2.14 REMARK 500 OE1 GLU H 46 O HOH H 716 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 92 CB CYS H 92 SG -0.123 REMARK 500 SER H 229 C SER H 229 O 0.975 REMARK 500 ILE P 309 C GLY P 312 N 0.284 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 LYS H 129 N - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 SER H 229 CA - C - O ANGL. DEV. = -65.5 DEGREES REMARK 500 ILE P 309 O - C - N ANGL. DEV. = -11.5 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 ASN L 27B -86.82 -136.71 REMARK 500 ASN L 51 -54.70 81.28 REMARK 500 ASP L 52 17.48 -152.90 REMARK 500 ASP L 151 -121.02 55.02 REMARK 500 ASP H 100E -10.36 -168.03 REMARK 500 SER H 127 -23.57 -38.11 REMARK 500 SER H 128 -140.50 102.97 REMARK 500 SER H 130 101.59 -4.41 REMARK 500 ASP H 146 69.02 63.10 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 SER H 134 GLY H 135 142.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE P 309 16.01 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 EDO L 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO H 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY H 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY H 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY L 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B1A RELATED DB: PDB REMARK 900 THE SAME FAB COMPLEXES WITH UG1033 PEPTIDE REMARK 900 RELATED ID: 2B1H RELATED DB: PDB REMARK 900 THE SAME FAB COMPLEXES WITH UG29 PEPTIDE DBREF 2B0S P 303 320 UNP P05877 ENV_HV1MN 308 325 DBREF 2B0S L 1 212 PDB 2B0S 2B0S 1 212 DBREF 2B0S H 1 229 PDB 2B0S 2B0S 1 229 SEQADV 2B0S ALA P 323 UNP P05877 INSERTION SEQRES 1 L 215 GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 L 215 PRO GLY GLN ARG ILE SER ILE SER CYS SER GLY THR SER SEQRES 3 L 215 SER ASN VAL GLU ASN ASN TYR VAL TYR TRP TYR GLN HIS SEQRES 4 L 215 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR ARG ASN SEQRES 5 L 215 ASP HIS ARG SER SER GLY ILE PRO ASP ARG PHE SER ALA SEQRES 6 L 215 SER LYS SER GLY THR SER ALA SER LEU ALA ILE SER GLY SEQRES 7 L 215 LEU ARG PRO GLU ASP GLU GLY ASP TYR TYR CYS ALA ALA SEQRES 8 L 215 TRP ASP ASP SER ARG GLY GLY PRO ASP TRP VAL PHE GLY SEQRES 9 L 215 GLY GLY THR LYS LEU THR VAL LEU ALA GLN PRO LYS ALA SEQRES 10 L 215 ALA PRO SER VAL THR LEU PHE PRO PRO SER SER GLU GLU SEQRES 11 L 215 LEU GLN ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER SEQRES 12 L 215 ASP PHE TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA SEQRES 13 L 215 ASP SER SER PRO VAL LYS ALA GLY VAL GLU THR THR THR SEQRES 14 L 215 PRO SER LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER SEQRES 15 L 215 TYR LEU SER LEU THR PRO GLU GLN TRP LYS SER HIS LYS SEQRES 16 L 215 SER TYR SER CYS GLN VAL THR HIS GLU GLY SER THR VAL SEQRES 17 L 215 GLU LYS THR VAL ALA PRO THR SEQRES 1 H 226 GLU ILE GLN LEU GLU GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 226 SER GLY GLU SER LEU LYS ILE SER CYS GLN THR SER GLY SEQRES 3 H 226 TYR SER PHE SER ASP TYR TRP ILE GLY TRP VAL ARG GLN SEQRES 4 H 226 MET PRO GLY LYS GLY LEU GLU TRP MET GLY ILE PHE TYR SEQRES 5 H 226 PRO GLY ASP SER ASP SER ARG TYR SER PRO SER PHE GLU SEQRES 6 H 226 GLY GLN VAL THR MET SER ALA ASP ARG SER THR ASN THR SEQRES 7 H 226 ALA HIS LEU GLN TRP SER SER LEU LYS PRO SER ASP THR SEQRES 8 H 226 ALA LEU TYR TYR CYS ALA ARG LEU GLY GLY ASP TYR GLU SEQRES 9 H 226 ASP SER GLY ALA ASP ALA PHE ASP PHE TRP GLY GLN GLY SEQRES 10 H 226 THR LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SEQRES 11 H 226 SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER SEQRES 12 H 226 GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR SEQRES 13 H 226 PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA SEQRES 14 H 226 LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SEQRES 15 H 226 SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL SEQRES 16 H 226 PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN SEQRES 17 H 226 VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS SEQRES 18 H 226 VAL GLU PRO LYS SER SEQRES 1 P 19 LYS ARG LYS ARG ILE HIS ILE GLY PRO GLY ARG ALA PHE SEQRES 2 P 19 TYR THR THR LYS ASN ALA HET EDO L 702 4 HET ACY L 503 4 HET EDO H 703 4 HET ACY H 501 4 HET ACY H 502 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM ACY ACETIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO 2(C2 H6 O2) FORMUL 5 ACY 3(C2 H4 O2) FORMUL 9 HOH *191(H2 O) HELIX 1 1 ARG L 79 GLU L 83 5 5 HELIX 2 2 SER L 121 ALA L 127 1 7 HELIX 3 3 THR L 182 HIS L 189 1 8 HELIX 4 4 SER H 28 TYR H 32 5 5 HELIX 5 5 LYS H 83 THR H 87 5 5 HELIX 6 6 SER H 163 ALA H 165 5 3 HELIX 7 7 SER H 196 LEU H 198 5 3 HELIX 8 8 LYS H 213 ASN H 216 5 4 SHEET 1 A 6 SER L 9 GLY L 13 0 SHEET 2 A 6 THR L 102 VAL L 106 1 O THR L 105 N ALA L 11 SHEET 3 A 6 GLY L 84 ASP L 92 -1 N GLY L 84 O LEU L 104 SHEET 4 A 6 VAL L 33 HIS L 38 -1 N HIS L 38 O ASP L 85 SHEET 5 A 6 LYS L 45 TYR L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 A 6 HIS L 53 ARG L 54 -1 O HIS L 53 N TYR L 49 SHEET 1 B 4 SER L 9 GLY L 13 0 SHEET 2 B 4 THR L 102 VAL L 106 1 O THR L 105 N ALA L 11 SHEET 3 B 4 GLY L 84 ASP L 92 -1 N GLY L 84 O LEU L 104 SHEET 4 B 4 ASP L 95D PHE L 98 -1 O ASP L 95D N ASP L 92 SHEET 1 C 3 ILE L 19 SER L 24 0 SHEET 2 C 3 SER L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 3 C 3 PHE L 62 SER L 67 -1 N SER L 63 O ALA L 74 SHEET 1 D 4 SER L 114 PHE L 118 0 SHEET 2 D 4 ALA L 130 PHE L 139 -1 O SER L 137 N SER L 114 SHEET 3 D 4 TYR L 173 LEU L 181 -1 O ALA L 175 N ILE L 136 SHEET 4 D 4 VAL L 159 THR L 161 -1 N GLU L 160 O TYR L 178 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 173 LEU L 181 -1 O ALA L 175 N ILE L 136 SHEET 4 E 4 SER L 165 LYS L 166 -1 N SER L 165 O ALA L 174 SHEET 1 F 4 SER L 153 VAL L 155 0 SHEET 2 F 4 THR L 145 ALA L 150 -1 N ALA L 150 O SER L 153 SHEET 3 F 4 TYR L 192 HIS L 198 -1 O THR L 197 N THR L 145 SHEET 4 F 4 SER L 203 VAL L 209 -1 O LYS L 207 N CYS L 194 SHEET 1 G 4 GLN H 3 GLN H 6 0 SHEET 2 G 4 LEU H 18 SER H 25 -1 O GLN H 23 N GLU H 5 SHEET 3 G 4 THR H 77 TRP H 82 -1 O TRP H 82 N LEU H 18 SHEET 4 G 4 THR H 68 ASP H 72 -1 N SER H 70 O HIS H 79 SHEET 1 H 6 GLU H 10 LYS H 13 0 SHEET 2 H 6 THR H 107 SER H 112 1 O THR H 110 N LYS H 12 SHEET 3 H 6 ALA H 88 GLY H 96 -1 N TYR H 90 O THR H 107 SHEET 4 H 6 ILE H 34 GLN H 39 -1 N GLY H 35 O ALA H 93 SHEET 5 H 6 LEU H 45 PHE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 H 6 SER H 57 TYR H 59 -1 O ARG H 58 N ILE H 50 SHEET 1 I 4 GLU H 10 LYS H 13 0 SHEET 2 I 4 THR H 107 SER H 112 1 O THR H 110 N LYS H 12 SHEET 3 I 4 ALA H 88 GLY H 96 -1 N TYR H 90 O THR H 107 SHEET 4 I 4 ALA H 100F TRP H 103 -1 O ALA H 100F N GLY H 96 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 THR H 137 TYR H 147 -1 O GLY H 141 N LEU H 124 SHEET 3 J 4 TYR H 185 PRO H 194 -1 O VAL H 191 N LEU H 140 SHEET 4 J 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 190 SHEET 1 K 4 SER H 120 LEU H 124 0 SHEET 2 K 4 THR H 137 TYR H 147 -1 O GLY H 141 N LEU H 124 SHEET 3 K 4 TYR H 185 PRO H 194 -1 O VAL H 191 N LEU H 140 SHEET 4 K 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 186 SHEET 1 L 3 THR H 153 TRP H 157 0 SHEET 2 L 3 ILE H 207 HIS H 212 -1 O ASN H 209 N SER H 156 SHEET 3 L 3 THR H 217 LYS H 222 -1 O VAL H 219 N VAL H 210 SHEET 1 M 2 ILE P 307 GLY P 312 0 SHEET 2 M 2 ARG P 315 PHE P 317 -1 O PHE P 317 N ILE P 307 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.10 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.07 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.09 SSBOND 4 CYS H 142 CYS H 208 1555 1555 2.06 CISPEP 1 TYR L 140 PRO L 141 0 0.09 CISPEP 2 PHE H 148 PRO H 149 0 -8.81 CISPEP 3 GLU H 150 PRO H 151 0 -5.98 SITE 1 AC1 3 HIS L 38 PRO L 40 ASP L 85 SITE 1 AC2 5 GLY H 8 ALA H 9 ILE H 207 ASP H 220 SITE 2 AC2 5 HOH H 772 SITE 1 AC3 3 ARG H 38 SER H 62 PHE H 63 SITE 1 AC4 6 VAL H 177 GLN H 179 SER H 186 TYR L 178 SITE 2 AC4 6 SER L 180 HOH L 717 SITE 1 AC5 6 GLN L 37 LYS L 45 LEU L 47 ILE L 58 SITE 2 AC5 6 PHE L 62 HOH L 708 CRYST1 60.471 60.471 275.194 90.00 90.00 90.00 P 41 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 0.016537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016537 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003634 0.00000