PDB Short entry for 3WI4 HEADER MEMBRANE PROTEIN 05-SEP-13 3WI4 TITLE CRYSTAL STRUCTURE OF WILD-TYPE PORB FROM NEISSERIA MENINGITIDIS TITLE 2 SEROGROUP B COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR OUTER MEMBRANE PROTEIN P.IB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PIB, PROTEIN IB, CLASS 3 PROTEIN, PORIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 122586; SOURCE 4 STRAIN: MC58; SOURCE 5 GENE: PORB, NMB2039; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-BARREL, PORIN, OUTER MEMBRANE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.KATTNER,D.TOUSSI,L.M.WETZLER,N.RUPPEL,P.MASSARI,M.TANABE REVDAT 2 12-MAR-14 3WI4 1 JRNL REVDAT 1 01-JAN-14 3WI4 0 JRNL AUTH C.KATTNER,D.N.TOUSSI,J.ZAUCHA,L.M.WETZLER,N.RUPPEL, JRNL AUTH 2 U.ZACHARIAE,P.MASSARI,M.TANABE JRNL TITL CRYSTALLOGRAPHIC ANALYSIS OF NEISSERIA MENINGITIDIS PORB JRNL TITL 2 EXTRACELLULAR LOOPS POTENTIALLY IMPLICATED IN TLR2 JRNL TITL 3 RECOGNITION. JRNL REF J.STRUCT.BIOL. V. 185 440 2014 JRNL REFN ISSN 1047-8477 JRNL PMID 24361688 JRNL DOI 10.1016/J.JSB.2013.12.006 REMARK 2 REMARK 2 RESOLUTION. 3.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 3.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 50.0 REMARK 3 NUMBER OF REFLECTIONS : 4948 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) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 535 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) : 3.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 233 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2372 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.15000 REMARK 3 B12 (A**2) : 0.05000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.745 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.872 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.844 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2428 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3281 ; 1.938 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 309 ; 6.793 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;36.810 ;24.553 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 386 ;25.899 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;27.355 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 345 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1902 ; 0.007 ; 0.020 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 3WI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-SEP-13. REMARK 100 THE RCSB ID CODE IS RCSB096363. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : TOROIDAL MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6628 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 80.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.5-7.0, 50MM CSCL, 35% REMARK 280 (V/V) JEFFAMINE M-600, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 74.14550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.80792 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.68167 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 74.14550 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 42.80792 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.68167 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 74.14550 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 42.80792 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.68167 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 74.14550 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 42.80792 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.68167 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 74.14550 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 42.80792 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.68167 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 74.14550 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 42.80792 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 34.68167 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 85.61585 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 69.36333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 85.61585 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 69.36333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 85.61585 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 69.36333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 85.61585 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 69.36333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 85.61585 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 69.36333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 85.61585 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 69.36333 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: 6890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 MET A 1 REMARK 465 GLU A 186 REMARK 465 GLY A 187 REMARK 465 LEU A 188 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 OD2 ASP A 100 NH2 ARG A 130 2.11 REMARK 500 N SER A 65 OD2 ASP A 70 2.16 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 ASN A 23 CB - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 ALA A 206 CB - CA - C ANGL. DEV. = -23.9 DEGREES REMARK 500 LEU A 207 N - CA - CB ANGL. DEV. = 25.1 DEGREES REMARK 500 ASP A 222 N - CA - C ANGL. DEV. = 20.2 DEGREES REMARK 500 LEU A 257 N - CA - C ANGL. DEV. = -18.5 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 GLU A 28 117.30 -167.84 REMARK 500 ARG A 76 -156.18 -105.39 REMARK 500 LEU A 207 109.04 179.37 REMARK 500 ASN A 225 59.01 31.24 REMARK 500 VAL A 258 -146.30 -119.82 REMARK 500 ASP A 260 -72.29 -122.24 REMARK 500 LYS A 299 -159.67 -100.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 207 20.7 L L OUTSIDE RANGE REMARK 500 ASP A 222 22.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WI5 RELATED DB: PDB DBREF 3WI4 A 2 313 UNP P30690 OMPB1_NEIMB 20 331 SEQADV 3WI4 MET A 1 UNP P30690 INITIATING METHIONINE SEQRES 1 A 313 MET ASP VAL THR LEU TYR GLY THR ILE LYS ALA GLY VAL SEQRES 2 A 313 GLU THR SER ARG SER VAL PHE HIS GLN ASN GLY GLN VAL SEQRES 3 A 313 THR GLU VAL THR THR ALA THR GLY ILE VAL ASP LEU GLY SEQRES 4 A 313 SER LYS ILE GLY PHE LYS GLY GLN GLU ASP LEU GLY ASN SEQRES 5 A 313 GLY LEU LYS ALA ILE TRP GLN VAL GLU GLN LYS ALA SER SEQRES 6 A 313 ILE ALA GLY THR ASP SER GLY TRP GLY ASN ARG GLN SER SEQRES 7 A 313 PHE ILE GLY LEU LYS GLY GLY PHE GLY LYS LEU ARG VAL SEQRES 8 A 313 GLY ARG LEU ASN SER VAL LEU LYS ASP THR GLY ASP ILE SEQRES 9 A 313 ASN PRO TRP ASP SER LYS SER ASP TYR LEU GLY VAL ASN SEQRES 10 A 313 LYS ILE ALA GLU PRO GLU ALA ARG LEU ILE SER VAL ARG SEQRES 11 A 313 TYR ASP SER PRO GLU PHE ALA GLY LEU SER GLY SER VAL SEQRES 12 A 313 GLN TYR ALA LEU ASN ASP ASN ALA GLY ARG HIS ASN SER SEQRES 13 A 313 GLU SER TYR HIS ALA GLY PHE ASN TYR LYS ASN GLY GLY SEQRES 14 A 313 PHE PHE VAL GLN TYR GLY GLY ALA TYR LYS ARG HIS HIS SEQRES 15 A 313 GLN VAL GLN GLU GLY LEU ASN ILE GLU LYS TYR GLN ILE SEQRES 16 A 313 HIS ARG LEU VAL SER GLY TYR ASP ASN ASP ALA LEU TYR SEQRES 17 A 313 ALA SER VAL ALA VAL GLN GLN GLN ASP ALA LYS LEU THR SEQRES 18 A 313 ASP ALA SER ASN SER HIS ASN SER GLN THR GLU VAL ALA SEQRES 19 A 313 ALA THR LEU ALA TYR ARG PHE GLY ASN VAL THR PRO ARG SEQRES 20 A 313 VAL SER TYR ALA HIS GLY PHE LYS GLY LEU VAL ASP ASP SEQRES 21 A 313 ALA ASP ILE GLY ASN GLU TYR ASP GLN VAL VAL VAL GLY SEQRES 22 A 313 ALA GLU TYR ASP PHE SER LYS ARG THR SER ALA LEU VAL SEQRES 23 A 313 SER ALA GLY TRP LEU GLN GLU GLY LYS GLY GLU ASN LYS SEQRES 24 A 313 PHE VAL ALA THR ALA GLY GLY VAL GLY LEU ARG HIS LYS SEQRES 25 A 313 PHE HELIX 1 1 SER A 96 GLY A 102 1 7 HELIX 2 2 VAL A 116 ALA A 120 5 5 HELIX 3 3 LEU A 147 GLY A 152 1 6 SHEET 1 A19 VAL A 26 VAL A 29 0 SHEET 2 A19 ALA A 32 ASP A 37 0 SHEET 3 A19 LYS A 41 GLY A 51 0 SHEET 4 A19 LEU A 54 LYS A 63 -1 O VAL A 60 N PHE A 44 SHEET 5 A19 SER A 78 GLY A 84 -1 O LYS A 83 N LYS A 55 SHEET 6 A19 GLY A 87 ASN A 95 -1 O GLY A 87 N GLY A 84 SHEET 7 A19 ARG A 125 ASP A 132 -1 O LEU A 126 N LEU A 94 SHEET 8 A19 LEU A 139 ALA A 146 -1 O VAL A 143 N TYR A 131 SHEET 9 A19 SER A 158 ASN A 167 -1 O HIS A 160 N GLN A 144 SHEET 10 A19 PHE A 170 HIS A 181 -1 O VAL A 172 N TYR A 165 SHEET 11 A19 ILE A 190 ASN A 204 -1 O VAL A 199 N GLN A 173 SHEET 12 A19 LEU A 207 LEU A 220 -1 O ASP A 217 N GLN A 194 SHEET 13 A19 HIS A 227 ALA A 238 -1 O ALA A 238 N TYR A 208 SHEET 14 A19 ARG A 247 GLY A 253 -1 O TYR A 250 N ALA A 235 SHEET 15 A19 TYR A 267 ASP A 277 -1 O GLY A 273 N ARG A 247 SHEET 16 A19 THR A 282 GLU A 293 -1 O ALA A 284 N TYR A 276 SHEET 17 A19 PHE A 300 PHE A 313 -1 O GLY A 306 N SER A 287 SHEET 18 A19 VAL A 3 HIS A 21 -1 N VAL A 19 O VAL A 301 SHEET 19 A19 ALA A 32 ASP A 37 -1 O ALA A 32 N SER A 16 CRYST1 148.291 148.291 104.045 90.00 90.00 120.00 H 3 2 18 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 0.006743 0.003893 0.000000 0.00000 SCALE2 0.000000 0.007787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009611 0.00000