HEADER IMMUNE SYSTEM 08-DEC-11 3V0W TITLE CRYSTAL STRUCTURE OF FAB WN1 222-5 IN COMPLEX WITH LPS COMPND MOL_ID: 1; COMPND 2 MOLECULE: WN1 222-5 FAB (IGG2A) LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: WN1 222-5 FAB (IGG2A) HEAVY CHAIN; COMPND 6 CHAIN: H SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: NZB; SOURCE 6 CELL: HYBRIDOMA; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 STRAIN: NZB; SOURCE 12 CELL: HYBRIDOMA KEYWDS BETA BARREL, ANTIBODY, FAB, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.GOMERY,S.V.EVANS REVDAT 3 08-NOV-17 3V0W 1 REMARK REVDAT 2 02-JAN-13 3V0W 1 JRNL REVDAT 1 05-DEC-12 3V0W 0 JRNL AUTH K.GOMERY,S.MULLER-LOENNIES,C.L.BROOKS,L.BRADE,P.KOSMA, JRNL AUTH 2 F.DI PADOVA,H.BRADE,S.V.EVANS JRNL TITL ANTIBODY WN1 222-5 MIMICS TOLL-LIKE RECEPTOR 4 BINDING IN JRNL TITL 2 THE RECOGNITION OF LPS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 20877 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23184990 JRNL DOI 10.1073/PNAS.1209253109 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 61638 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3288 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4366 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 234 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3244 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 183 REMARK 3 SOLVENT ATOMS : 526 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.61000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.795 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3V0W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VERTICAL FOCUSSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65161 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.25600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, AMMONIUM SULFATE, PH REMARK 280 4.6, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.26600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.92600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.92600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.89900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.92600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.92600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.63300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.92600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.92600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 88.89900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.92600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.92600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.63300 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 59.26600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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 L 212 REMARK 465 CYS H 128 REMARK 465 GLY H 129 REMARK 465 ASP H 130 REMARK 465 THR H 131 REMARK 465 THR H 132 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 NE ARG H 52 O HOH H 448 1.24 REMARK 500 O HOH H 401 O HOH H 554 1.53 REMARK 500 O8 GM0 H 308 O HOH H 605 1.57 REMARK 500 O GLN H 95 O HOH H 536 1.62 REMARK 500 CZ ARG H 52 O HOH H 448 1.63 REMARK 500 ND2 ASN H 82A O HOH H 436 1.67 REMARK 500 CB ASN H 82A O HOH H 444 1.77 REMARK 500 NH2 ARG H 52 O HOH H 448 1.90 REMARK 500 CG ASN H 82A O HOH H 436 1.91 REMARK 500 O HOH H 403 O HOH H 410 1.92 REMARK 500 O9 GM0 H 306 O HOH H 448 1.97 REMARK 500 O HOH L 407 O HOH L 439 1.99 REMARK 500 P GM0 H 308 O HOH H 605 2.03 REMARK 500 O4 GM0 H 308 O HOH H 605 2.14 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 CD LYS H 52B O HOH L 513 4545 1.78 REMARK 500 O HOH L 588 O HOH H 583 5444 2.09 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 30 -123.34 56.34 REMARK 500 ALA L 51 -37.93 71.82 REMARK 500 PRO L 59 141.06 -31.82 REMARK 500 SER H 134 -66.95 98.61 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 L 7 PRO L 8 -36.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 SUGARS H 301-310 ARE THE OBSERVED REGION OF THE NATURALLY OCCURING REMARK 600 LIPOPOLYSACCHARIDE FROM THE OUTER MEMBRANE OF GRAM-NEGATIVE BACTERIA REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PA1 H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC H 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLA H 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GM0 H 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GMH H 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GM0 H 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KDO H 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KDO H 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 316 DBREF 3V0W L 1 212 PDB 3V0W 3V0W 1 212 DBREF 3V0W H 1 212 PDB 3V0W 3V0W 1 212 SEQRES 1 L 212 ASP ILE GLN MET ASN GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 212 SER LEU GLY ASP THR ILE SER ILE THR CYS ARG ALA SER SEQRES 3 L 212 GLN ASN ILE ASN ILE TRP LEU SER TRP TYR GLN GLN LYS SEQRES 4 L 212 PRO GLY ASN VAL PRO LYS LEU LEU ILE TYR LYS ALA SER SEQRES 5 L 212 ASN LEU HIS THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 212 GLY SER GLY THR ASP PHE THR LEU ILE ILE SER SER LEU SEQRES 7 L 212 GLN PRO GLU ASP ILE ALA THR TYR TYR CYS LEU GLN GLY SEQRES 8 L 212 GLN SER TYR PRO ARG THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 212 GLU ILE LYS ARG GLY ASP ALA ALA PRO THR VAL SER ILE SEQRES 10 L 212 PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SEQRES 11 L 212 SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP SEQRES 12 L 212 ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN SEQRES 13 L 212 ASN GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS SEQRES 14 L 212 ASP SER THR TYR SER MET SER SER THR LEU THR LEU THR SEQRES 15 L 212 LYS ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU SEQRES 16 L 212 ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER SEQRES 17 L 212 PHE ASN ARG GLY SEQRES 1 H 219 GLU VAL LYS LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 219 PRO GLY GLY SER LEU SER LEU SER CYS ALA ALA SER GLY SEQRES 3 H 219 PHE THR PHE SER ASP TYR TYR MET THR TRP VAL ARG GLN SEQRES 4 H 219 ALA PRO GLY LYS ALA PRO GLU TRP LEU ALA LEU ILE ARG SEQRES 5 H 219 ASN LYS ARG ASN GLY ASP THR ALA GLU TYR SER ALA SER SEQRES 6 H 219 VAL LYS GLY ARG PHE THR ILE SER ARG ASP TYR SER ARG SEQRES 7 H 219 SER ILE LEU HIS LEU GLN MET ASN ALA LEU ARG THR GLU SEQRES 8 H 219 ASP SER ALA THR TYR TYR CYS VAL ARG GLN GLY ARG GLY SEQRES 9 H 219 TYR THR LEU ASP TYR TRP GLY GLN GLY THR SER VAL THR SEQRES 10 H 219 VAL SER SER ALA LYS THR THR ALA PRO SER VAL TYR PRO SEQRES 11 H 219 LEU ALA PRO VAL CYS GLY ASP THR THR GLY SER SER VAL SEQRES 12 H 219 THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO SEQRES 13 H 219 VAL THR LEU THR TRP ASN SER GLY SER LEU SER SER GLY SEQRES 14 H 219 VAL HIS THR PHE PRO ALA VAL LEU GLN SER GLY LEU TYR SEQRES 15 H 219 THR LEU SER SER SER VAL THR VAL THR SER SER THR TRP SEQRES 16 H 219 PRO SER GLN SER ILE THR CYS ASN VAL ALA HIS PRO ALA SEQRES 17 H 219 SER SER THR LYS VAL ASP LYS LYS ILE GLU PRO HET SO4 L 301 5 HET SO4 L 302 5 HET SO4 L 303 5 HET SO4 L 304 5 HET PA1 H 301 11 HET GLC H 302 11 HET GLC H 303 11 HET GLC H 304 11 HET GLA H 305 11 HET GM0 H 306 17 HET GMH H 307 13 HET GM0 H 308 17 HET KDO H 309 16 HET KDO H 310 15 HET SO4 H 311 5 HET SO4 H 312 5 HET SO4 H 313 5 HET SO4 H 314 5 HET SO4 H 315 5 HET SO4 H 316 5 HETNAM SO4 SULFATE ION HETNAM PA1 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM GLC ALPHA-D-GLUCOSE HETNAM GLA ALPHA D-GALACTOSE HETNAM GM0 4-O-PHOSPHONO-L-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE HETNAM GMH L-GLYCERO-D-MANNO-HEPTOPYRANOSE HETNAM KDO 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID FORMUL 3 SO4 10(O4 S 2-) FORMUL 7 PA1 C6 H13 N O5 FORMUL 7 GLC 3(C6 H12 O6) FORMUL 7 GLA C6 H12 O6 FORMUL 8 GM0 2(C7 H15 O10 P) FORMUL 9 GMH C7 H14 O7 FORMUL 11 KDO 2(C8 H14 O8) FORMUL 18 HOH *526(H2 O) HELIX 1 1 GLN L 79 ILE L 83 5 5 HELIX 2 2 SER L 121 SER L 127 1 7 HELIX 3 3 LYS L 183 GLU L 187 1 5 HELIX 4 4 THR H 28 TYR H 32 5 5 HELIX 5 5 ASN H 52A GLY H 54 5 5 HELIX 6 6 ARG H 83 SER H 87 5 5 HELIX 7 7 SER H 156 SER H 158 5 3 HELIX 8 8 PRO H 200 SER H 203 5 4 SHEET 1 A 4 MET L 4 SER L 7 0 SHEET 2 A 4 ILE L 19 ALA L 25 -1 O ARG L 24 N ASN L 5 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 A 4 PHE L 62 SER L 67 -1 N SER L 63 O ILE L 74 SHEET 1 B 6 SER L 10 ALA L 13 0 SHEET 2 B 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 B 6 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 B 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 B 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 B 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 C 4 SER L 10 ALA L 13 0 SHEET 2 C 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 C 4 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 C 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 D 4 THR L 114 PHE L 118 0 SHEET 2 D 4 GLY L 129 PHE L 139 -1 O ASN L 137 N THR L 114 SHEET 3 D 4 TYR L 173 THR L 182 -1 O MET L 175 N LEU L 136 SHEET 4 D 4 VAL L 159 TRP L 163 -1 N SER L 162 O SER L 176 SHEET 1 E 4 SER L 153 ARG L 155 0 SHEET 2 E 4 ILE L 144 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 E 4 SER L 191 HIS L 198 -1 O THR L 197 N ASN L 145 SHEET 4 E 4 ILE L 205 ASN L 210 -1 O PHE L 209 N TYR L 192 SHEET 1 F 4 LYS H 3 SER H 7 0 SHEET 2 F 4 LEU H 18 SER H 25 -1 O SER H 25 N LYS H 3 SHEET 3 F 4 ILE H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 F 4 PHE H 67 ASP H 72 -1 N SER H 70 O HIS H 79 SHEET 1 G 6 LEU H 11 VAL H 12 0 SHEET 2 G 6 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 G 6 ALA H 88 GLN H 95 -1 N TYR H 90 O THR H 107 SHEET 4 G 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 G 6 GLU H 46 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 G 6 ALA H 57 TYR H 59 -1 O GLU H 58 N LEU H 50 SHEET 1 H 4 LEU H 11 VAL H 12 0 SHEET 2 H 4 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 H 4 ALA H 88 GLN H 95 -1 N TYR H 90 O THR H 107 SHEET 4 H 4 LEU H 100A TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 I 4 SER H 120 LEU H 124 0 SHEET 2 I 4 SER H 135 TYR H 145 -1 O LEU H 141 N TYR H 122 SHEET 3 I 4 LEU H 174 THR H 184 -1 O LEU H 177 N VAL H 142 SHEET 4 I 4 VAL H 163 THR H 165 -1 N HIS H 164 O SER H 180 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 SER H 135 TYR H 145 -1 O LEU H 141 N TYR H 122 SHEET 3 J 4 LEU H 174 THR H 184 -1 O LEU H 177 N VAL H 142 SHEET 4 J 4 VAL H 169 GLN H 171 -1 N VAL H 169 O THR H 176 SHEET 1 K 3 THR H 151 TRP H 154 0 SHEET 2 K 3 THR H 194 HIS H 199 -1 O ALA H 198 N THR H 151 SHEET 3 K 3 THR H 204 LYS H 209 -1 O THR H 204 N HIS H 199 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.16 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.08 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.06 SSBOND 4 CYS H 140 CYS H 195 1555 1555 2.04 LINK C1 GLC H 303 O3 GLC H 304 1555 1555 1.35 LINK C1 GLC H 302 O2 GLC H 303 1555 1555 1.41 LINK O6 GLC H 304 C1 GLA H 305 1555 1555 1.43 LINK C1 PA1 H 301 O2 GLC H 302 1555 1555 1.46 LINK O4 KDO H 309 C2 KDO H 310 1555 1555 1.50 LINK C1 GM0 H 308 O5 KDO H 309 1555 1555 1.42 LINK C1 GLC H 304 O3 GM0 H 306 1555 1555 1.44 LINK C1 GM0 H 306 O3 GM0 H 308 1555 1555 1.47 LINK O7 GM0 H 306 C1 GMH H 307 1555 1555 1.39 CISPEP 1 TYR L 94 PRO L 95 0 4.13 CISPEP 2 TYR L 140 PRO L 141 0 7.20 CISPEP 3 PHE H 146 PRO H 147 0 -6.01 CISPEP 4 GLU H 148 PRO H 149 0 7.19 CISPEP 5 TRP H 188 PRO H 189 0 5.91 SITE 1 AC1 4 LYS L 39 LYS L 45 HOH L 432 HOH L 600 SITE 1 AC2 5 SER H 161 GLY H 162 LYS L 169 HOH L 492 SITE 2 AC2 5 HOH L 508 SITE 1 AC3 4 SER H 70 HIS H 79 LEU L 11 HOH L 480 SITE 1 AC4 5 PA1 H 301 ASN L 28 ASN L 30 GLN L 92 SITE 2 AC4 5 HOH L 482 SITE 1 AC5 6 GLC H 302 GLC H 304 GM0 H 306 HOH H 433 SITE 2 AC5 6 HOH H 650 SO4 L 304 SITE 1 AC6 4 PA1 H 301 GLC H 303 GLC H 304 HOH H 575 SITE 1 AC7 5 GLC H 302 GLC H 304 HOH H 509 HOH H 566 SITE 2 AC7 5 HOH H 666 SITE 1 AC8 9 ARG H 52 ASN H 53 PA1 H 301 GLC H 302 SITE 2 AC8 9 GLC H 303 GLA H 305 GM0 H 306 HOH H 448 SITE 3 AC8 9 HOH H 535 SITE 1 AC9 11 ARG H 52C ASN H 53 GLC H 304 GM0 H 306 SITE 2 AC9 11 GM0 H 308 HOH H 434 HOH H 535 HOH H 624 SITE 3 AC9 11 GLN L 3 ASN L 5 SER L 26 SITE 1 BC1 17 TYR H 33 ARG H 52 TYR H 99 PA1 H 301 SITE 2 BC1 17 GLC H 304 GLA H 305 GMH H 307 GM0 H 308 SITE 3 BC1 17 KDO H 310 HOH H 402 HOH H 406 HOH H 443 SITE 4 BC1 17 HOH H 448 HOH H 481 HOH H 484 HOH H 492 SITE 5 BC1 17 TYR L 94 SITE 1 BC2 11 TYR H 33 GLN H 95 GLY H 96 ARG H 97 SITE 2 BC2 11 GLY H 98 TYR H 99 GM0 H 306 KDO H 309 SITE 3 BC2 11 HOH H 441 HOH H 475 HOH H 559 SITE 1 BC3 12 ARG H 52C ASN H 53 GLA H 305 GM0 H 306 SITE 2 BC3 12 KDO H 309 KDO H 310 HOH H 406 HOH H 559 SITE 3 BC3 12 HOH H 605 HOH H 624 HOH H 634 HOH H 659 SITE 1 BC4 9 ARG H 52C ARG H 97 GMH H 307 GM0 H 308 SITE 2 BC4 9 KDO H 310 HOH H 441 HOH H 506 HOH H 596 SITE 3 BC4 9 HOH H 653 SITE 1 BC5 6 TYR H 99 GM0 H 306 GM0 H 308 KDO H 309 SITE 2 BC5 6 HOH H 412 HOH H 627 SITE 1 BC6 7 LYS H 52B TYR H 73 THR H 204 LYS H 205 SITE 2 BC6 7 HOH H 516 ARG L 24 HOH L 418 SITE 1 BC7 10 PHE H 27 THR H 28 PHE H 29 SER H 30 SITE 2 BC7 10 LYS H 205 HOH H 413 HOH H 542 HOH H 562 SITE 3 BC7 10 HOH H 620 HOH H 668 SITE 1 BC8 8 GLN H 13 HOH H 419 HOH H 474 HOH H 489 SITE 2 BC8 8 HOH H 583 LYS L 199 HOH L 567 HOH L 577 SITE 1 BC9 3 TYR H 32 ARG H 94 HOH H 527 SITE 1 CC1 8 GLY H 15 ARG H 83 ASP L 143 THR L 197 SITE 2 CC1 8 HIS L 198 LYS L 199 HOH L 402 HOH L 498 SITE 1 CC2 6 LYS H 43 ALA H 44 HOH H 500 HOH H 628 SITE 2 CC2 6 GLY L 100 HOH L 561 CRYST1 101.852 101.852 118.532 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009818 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008437 0.00000