HEADER MEMBRANE PROTEIN 04-JUN-09 3A2R OBSLTE 07-NOV-12 3A2R 3VZT TITLE CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEIN PORB FROM NEISSERIA TITLE 2 MENINGITIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN II; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 GENE: PORB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) DERIVATIVE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21BPORB KEYWDS BETA BARREL, OUTER MEMBRANE PROTEIN, PORIN, NEISSERIA MENINGITIDIS, KEYWDS 2 CELL MEMBRANE, CELL OUTER MEMBRANE, ION TRANSPORT, MEMBRANE, KEYWDS 3 TRANSMEMBRANE, TRANSPORT PROTEIN, IMMUNE SYSTEM, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.TANABE,T.M.IVERSON REVDAT 3 07-NOV-12 3A2R 1 OBSLTE VERSN REVDAT 2 16-JUN-10 3A2R 1 JRNL REVDAT 1 07-APR-10 3A2R 0 JRNL AUTH M.TANABE,C.M.NIMIGEAN,T.M.IVERSON JRNL TITL STRUCTURAL BASIS FOR SOLUTE TRANSPORT, NUCLEOTIDE JRNL TITL 2 REGULATION, AND IMMUNOLOGICAL RECOGNITION OF NEISSERIA JRNL TITL 3 MENINGITIDIS PORB. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 6811 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20351243 JRNL DOI 10.1073/PNAS.0912115107 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 16247 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 828 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) : 798 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2593 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.80000 REMARK 3 B22 (A**2) : 3.80000 REMARK 3 B33 (A**2) : -5.70000 REMARK 3 B12 (A**2) : 1.90000 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): 0.369 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.983 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2642 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3562 ; 1.519 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 9.154 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;38.086 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 431 ;17.481 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.708 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 374 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2047 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1058 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1779 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 144 ; 0.165 ; 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): 53 ; 0.209 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.087 ; 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): 1710 ; 0.864 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2636 ; 1.510 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1079 ; 1.943 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 926 ; 2.956 ; 4.500 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 3A2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-09. REMARK 100 THE RCSB ID CODE IS RCSB028738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17123 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 23.1000 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) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES, 50MM CSCL, 28-32% JEFFAMINE REMARK 280 M-600, PH6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.18550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.18550 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 53.18550 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: 8650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 83.05200 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 41.52600 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 71.92514 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH X 350 LIES ON A SPECIAL POSITION. 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 X -13 REMARK 465 ALA X -12 REMARK 465 SER X -11 REMARK 465 MET X -10 REMARK 465 THR X -9 REMARK 465 GLY X -8 REMARK 465 GLY X -7 REMARK 465 GLN X -6 REMARK 465 GLN X -5 REMARK 465 MET X -4 REMARK 465 GLY X -3 REMARK 465 ARG X -2 REMARK 465 ASP X -1 REMARK 465 LEU X 0 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 ASP X 296 N CA C O CB CG OD1 REMARK 480 ASP X 296 OD2 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 ND1 HIS X 279 OD1 ASP X 296 1.95 REMARK 500 O SER X 41 O ALA X 65 1.96 REMARK 500 NE2 GLN X 257 O TYR X 293 2.05 REMARK 500 O SER X 138 O HOH X 380 2.17 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 GLN X 1 C VAL X 2 N 0.139 REMARK 500 PRO X 139 CD PRO X 139 N -0.274 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 ALA X 65 CB - CA - C ANGL. DEV. = 14.9 DEGREES REMARK 500 ALA X 65 N - CA - C ANGL. DEV. = -24.6 DEGREES REMARK 500 SER X 66 N - CA - C ANGL. DEV. = -19.8 DEGREES REMARK 500 SER X 138 CB - CA - C ANGL. DEV. = 14.8 DEGREES REMARK 500 PRO X 139 CA - N - CD ANGL. DEV. = 10.8 DEGREES REMARK 500 PRO X 139 N - CA - CB ANGL. DEV. = -23.7 DEGREES REMARK 500 PRO X 139 N - CD - CG ANGL. DEV. = -22.3 DEGREES REMARK 500 PRO X 139 N - CA - C ANGL. DEV. = 16.5 DEGREES REMARK 500 PRO X 139 C - N - CD ANGL. DEV. = -31.4 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 VAL X 106 -31.18 -131.16 REMARK 500 SER X 138 -169.39 -78.03 REMARK 500 PRO X 139 125.70 -27.59 REMARK 500 ASP X 230 -6.97 74.78 REMARK 500 PHE X 268 77.92 -109.14 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 X 138 PRO X 139 89.03 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 GLN X 1 -11.09 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 ALA X 65 48.7 L L OUTSIDE RANGE REMARK 500 SER X 138 17.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A2S RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH SUCROSE REMARK 900 RELATED ID: 3A2T RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH GALACTOSE REMARK 900 RELATED ID: 3A2U RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AMP-PNP REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN REMARK 999 DOES NOT CURRENTLY EXIST. REMARK 999 THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. DBREF 3A2R X -13 341 PDB 3A2R 3A2R -13 341 SEQRES 1 X 355 MET ALA SER MET THR GLY GLY GLN GLN MET GLY ARG ASP SEQRES 2 X 355 LEU GLN VAL THR LEU TYR GLY THR ILE LYS ALA GLY VAL SEQRES 3 X 355 GLU VAL SER ARG VAL LYS ASP ALA GLY THR TYR LYS ALA SEQRES 4 X 355 GLN GLY GLY LYS SER LYS THR ALA THR GLN ILE ALA ASP SEQRES 5 X 355 PHE GLY SER LYS ILE GLY PHE LYS GLY GLN GLU ASP LEU SEQRES 6 X 355 GLY ASN GLY MET LYS ALA ILE TRP GLN LEU GLU GLN LYS SEQRES 7 X 355 ALA SER ILE ALA GLY THR ASN SER GLY TRP GLY ASN ARG SEQRES 8 X 355 GLN SER PHE ILE GLY LEU LYS GLY GLY PHE GLY THR VAL SEQRES 9 X 355 ARG ALA GLY ASN LEU ASN THR VAL LEU LYS ASP SER GLY SEQRES 10 X 355 ASP ASN VAL ASN ALA TRP GLU SER GLY SER ASN THR GLU SEQRES 11 X 355 ASP VAL LEU GLY LEU GLY THR ILE GLY ARG VAL GLU SER SEQRES 12 X 355 ARG GLU ILE SER VAL ARG TYR ASP SER PRO VAL PHE ALA SEQRES 13 X 355 GLY PHE SER GLY SER VAL GLN TYR VAL PRO ARG ASP ASN SEQRES 14 X 355 ALA ASN ASP VAL ASP LYS TYR LYS HIS THR LYS SER SER SEQRES 15 X 355 ARG GLU SER TYR HIS ALA GLY LEU LYS TYR GLU ASN ALA SEQRES 16 X 355 GLY PHE PHE GLY GLN TYR ALA GLY SER PHE ALA LYS TYR SEQRES 17 X 355 ALA ASP LEU ASN THR ASP ALA GLU ARG VAL ALA VAL ASN SEQRES 18 X 355 THR ALA ASN ALA HIS PRO VAL LYS ASP TYR GLN VAL HIS SEQRES 19 X 355 ARG VAL VAL ALA GLY TYR ASP ALA ASN ASP LEU TYR VAL SEQRES 20 X 355 SER VAL ALA GLY GLN TYR GLU ALA ALA LYS ASN ASN GLU SEQRES 21 X 355 VAL GLY SER ILE LYS GLY LYS LYS HIS GLU GLN THR GLN SEQRES 22 X 355 VAL ALA ALA THR ALA ALA TYR ARG PHE GLY ASN VAL THR SEQRES 23 X 355 PRO ARG VAL SER TYR ALA HIS GLY PHE LYS ALA LYS VAL SEQRES 24 X 355 ASN GLY VAL LYS ASP ALA ASN TYR GLN TYR ASP GLN VAL SEQRES 25 X 355 ILE VAL GLY ALA ASP TYR ASP PHE SER LYS ARG THR SER SEQRES 26 X 355 ALA LEU VAL SER ALA GLY TRP LEU LYS GLN GLY LYS GLY SEQRES 27 X 355 ALA GLY LYS VAL GLU GLN THR ALA SER MET VAL GLY LEU SEQRES 28 X 355 ARG HIS LYS PHE FORMUL 2 HOH *53(H2 O) HELIX 1 1 ALA X 25 LYS X 29 5 5 HELIX 2 2 THR X 97 GLY X 103 1 7 HELIX 3 3 ASP X 104 VAL X 106 5 3 HELIX 4 4 GLY X 112 GLU X 116 5 5 HELIX 5 5 LEU X 121 ARG X 126 1 6 HELIX 6 6 PRO X 152 ASN X 157 1 6 HELIX 7 7 ALA X 291 TYR X 293 5 3 SHEET 1 A18 ALA X 33 ASP X 38 0 SHEET 2 A18 VAL X 2 ASP X 19 -1 N GLY X 11 O ALA X 37 SHEET 3 A18 VAL X 328 PHE X 341 -1 O LEU X 337 N ALA X 10 SHEET 4 A18 THR X 310 GLN X 321 -1 N GLY X 317 O ALA X 332 SHEET 5 A18 TYR X 295 ASP X 305 -1 N TYR X 304 O ALA X 312 SHEET 6 A18 VAL X 271 GLY X 280 -1 N ARG X 274 O GLY X 301 SHEET 7 A18 LYS X 254 TYR X 266 -1 N ALA X 262 O TYR X 277 SHEET 8 A18 LEU X 231 ASN X 244 -1 N ALA X 242 O HIS X 255 SHEET 9 A18 HIS X 212 ALA X 228 -1 N LYS X 215 O LYS X 243 SHEET 10 A18 PHE X 183 LEU X 197 -1 N GLN X 186 O VAL X 223 SHEET 11 A18 SER X 171 ASN X 180 -1 N TYR X 178 O GLY X 185 SHEET 12 A18 PHE X 144 VAL X 151 -1 N GLN X 149 O HIS X 173 SHEET 13 A18 ARG X 130 ASP X 137 -1 N TYR X 136 O VAL X 148 SHEET 14 A18 GLY X 88 ASN X 96 -1 N ARG X 91 O ARG X 135 SHEET 15 A18 SER X 79 GLY X 85 -1 N LEU X 83 O VAL X 90 SHEET 16 A18 LYS X 56 LYS X 64 -1 N LYS X 56 O LYS X 84 SHEET 17 A18 LYS X 42 ASP X 50 -1 N PHE X 45 O LEU X 61 SHEET 18 A18 VAL X 2 ASP X 19 -1 N THR X 3 O LYS X 46 SHEET 1 B 2 ALA X 283 VAL X 285 0 SHEET 2 B 2 VAL X 288 ASP X 290 -1 O ASP X 290 N ALA X 283 CRYST1 83.052 83.052 106.371 90.00 90.00 120.00 P 63 6 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 0.012041 0.006952 0.000000 0.00000 SCALE2 0.000000 0.013903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009401 0.00000