HEADER MEMBRANE PROTEIN 18-NOV-11 3UPG TITLE LOOP DELETION MUTANT OF SALMONELLA TYPHI OSMOPORIN (OMPC):AN OUTER TITLE 2 MEMBRANE PROTEIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PORIN OMPC; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM; SOURCE 4 ORGANISM_TAXID: 90371; SOURCE 5 STRAIN: TY21A; SOURCE 6 GENE: OMPC, STM2267; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-21B(+) KEYWDS BETA BARREL, TRANSPORT PROTEIN, NON SPECIFIC PORIN, OSMOPORIN, OUTER KEYWDS 2 MEMBRANE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.PRASANTH,B.K.PUTCHA,A.AROCKIASAMY,S.KRISHNASWAMY REVDAT 2 01-NOV-23 3UPG 1 REMARK SEQADV LINK REVDAT 1 28-NOV-12 3UPG 0 JRNL AUTH P.PRASANTH,B.K.PUTCHA,A.AROCKIASAMY,S.KRISHNASWAMY JRNL TITL CRYSTAL STRUCTURE OF OSMOPORIN (OMPC) LOOP DELETION MUTANT: JRNL TITL 2 AN OUTER MEMBRANE PROTEIN FROM SALMONELLA TYPHI. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 13846 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) : 0.290 REMARK 3 R VALUE (WORKING SET) : 0.288 REMARK 3 FREE R VALUE : 0.325 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 730 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 968 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.4680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2406 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.28000 REMARK 3 B22 (A**2) : 5.28000 REMARK 3 B33 (A**2) : -7.92000 REMARK 3 B12 (A**2) : 2.64000 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): 0.730 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.446 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.459 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 62.001 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.820 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.858 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2459 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3330 ; 1.701 ; 1.921 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 308 ; 9.818 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;41.073 ;25.074 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 351 ;24.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;24.824 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 337 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1985 ; 0.006 ; 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): 1512 ; 0.792 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2382 ; 1.493 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 947 ; 1.502 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 948 ; 2.560 ; 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 : 1 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 : A 1 A 338 REMARK 3 ORIGIN FOR THE GROUP (A): 56.9813 -10.9717 -27.6936 REMARK 3 T TENSOR REMARK 3 T11: 0.4942 T22: 0.1786 REMARK 3 T33: 0.0116 T12: 0.0413 REMARK 3 T13: -0.0373 T23: -0.1268 REMARK 3 L TENSOR REMARK 3 L11: 1.3521 L22: 0.9963 REMARK 3 L33: 1.2737 L12: 0.4833 REMARK 3 L13: -0.3639 L23: 0.4479 REMARK 3 S TENSOR REMARK 3 S11: -0.0327 S12: -0.2054 S13: -0.0711 REMARK 3 S21: 0.0092 S22: -0.0549 S23: -0.0151 REMARK 3 S31: -0.2575 S32: 0.0317 S33: 0.0876 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: NULL REMARK 4 REMARK 4 3UPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 77.03 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97869 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14582 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 108.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2JN1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% POLYETHYLENE GLYCOL 3350, 0.2M REMARK 280 CALCIUM CHLORIDE DIHYDRATE, PH 5.1, MICROBATCH, TEMPERATURE REMARK 280 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 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 -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 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 108.36800 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 108.36800 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 108.36800 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 108.36800 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 108.36800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 108.36800 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: 9320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -179.0 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 57.57450 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -99.72196 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 115.14900 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 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 CL CL A 405 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 ASN A 153 REMARK 465 GLY A 154 REMARK 465 SER A 155 REMARK 465 LEU A 156 REMARK 465 LEU A 157 REMARK 465 ASN A 158 REMARK 465 GLN A 159 REMARK 465 ASN A 160 REMARK 465 ARG A 187 REMARK 465 THR A 188 REMARK 465 ALA A 189 REMARK 465 ASP A 190 REMARK 465 GLN A 191 REMARK 465 ASN A 192 REMARK 465 ASN A 193 REMARK 465 THR A 194 REMARK 465 ALA A 195 REMARK 465 ASN A 196 REMARK 465 ALA A 197 REMARK 465 ARG A 198 REMARK 465 LEU A 199 REMARK 465 TYR A 200 REMARK 465 GLY A 201 REMARK 465 ASN A 202 REMARK 465 GLY A 203 REMARK 465 ASP A 204 REMARK 465 ARG A 205 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 147 CD1 CD2 REMARK 470 PHE A 240 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 LYS A 269 CG CD CE NZ REMARK 470 TYR A 277 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 LYS A 315 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O TYR A 209 OG SER A 227 1.61 REMARK 500 O VAL A 46 O LEU A 50 1.88 REMARK 500 O SER A 280 N GLY A 282 2.11 REMARK 500 O ALA A 181 O HOH A 610 2.13 REMARK 500 O TYR A 164 O HOH A 605 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 47 N - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 26 113.01 -38.46 REMARK 500 SER A 29 -78.45 -123.43 REMARK 500 ASP A 30 119.56 -34.61 REMARK 500 ASN A 47 -158.68 176.41 REMARK 500 TRP A 56 128.36 -172.39 REMARK 500 ALA A 83 106.54 -52.59 REMARK 500 ASP A 84 -13.72 89.80 REMARK 500 GLU A 109 -69.10 -123.37 REMARK 500 ASP A 113 -31.49 48.84 REMARK 500 ASN A 119 58.07 -92.08 REMARK 500 MET A 121 -46.32 125.00 REMARK 500 GLN A 123 -130.46 -114.66 REMARK 500 ARG A 124 -172.76 -64.10 REMARK 500 PHE A 136 69.24 31.18 REMARK 500 LEU A 139 -72.69 -83.44 REMARK 500 ASP A 162 152.07 -44.26 REMARK 500 ILE A 172 81.59 -69.35 REMARK 500 GLU A 174 -126.50 38.58 REMARK 500 ALA A 217 -158.63 -141.25 REMARK 500 ASN A 218 90.78 -24.70 REMARK 500 ASN A 219 16.81 31.79 REMARK 500 TYR A 230 -84.08 -89.42 REMARK 500 THR A 233 -140.03 29.68 REMARK 500 ARG A 234 84.95 -9.12 REMARK 500 LEU A 259 121.89 170.13 REMARK 500 ASP A 272 90.22 2.81 REMARK 500 ALA A 279 -53.23 66.13 REMARK 500 SER A 280 -35.51 70.00 REMARK 500 TYR A 281 -27.43 29.91 REMARK 500 PHE A 298 -77.10 -67.89 REMARK 500 LYS A 315 103.79 -59.91 REMARK 500 ARG A 320 -82.50 -36.18 REMARK 500 GLN A 337 -163.46 -101.82 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 GLN A 45 VAL A 46 149.70 REMARK 500 VAL A 46 ASN A 47 77.57 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 VAL A 46 15.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 135 OD1 REMARK 620 2 HOH A 637 O 130.4 REMARK 620 3 HOH A 638 O 139.7 74.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 328 OD1 REMARK 620 2 HOH A 635 O 53.0 REMARK 620 3 HOH A 636 O 93.8 122.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 405 DBREF 3UPG A 1 338 UNP P0A263 OMPC_SALTY 22 378 SEQADV 3UPG A UNP P0A263 VAL 177 DELETION SEQADV 3UPG A UNP P0A263 SER 178 DELETION SEQADV 3UPG A UNP P0A263 GLY 179 DELETION SEQADV 3UPG A UNP P0A263 GLU 180 DELETION SEQADV 3UPG A UNP P0A263 ASN 181 DELETION SEQADV 3UPG A UNP P0A263 THR 182 DELETION SEQADV 3UPG A UNP P0A263 ASN 183 DELETION SEQADV 3UPG A UNP P0A263 GLY 184 DELETION SEQADV 3UPG A UNP P0A263 ARG 185 DELETION SEQADV 3UPG A UNP P0A263 SER 186 DELETION SEQADV 3UPG A UNP P0A263 ASN 270 DELETION SEQADV 3UPG A UNP P0A263 GLY 271 DELETION SEQADV 3UPG A UNP P0A263 SER 272 DELETION SEQADV 3UPG A UNP P0A263 ASN 273 DELETION SEQADV 3UPG A UNP P0A263 PRO 274 DELETION SEQADV 3UPG A UNP P0A263 SER 275 DELETION SEQADV 3UPG A UNP P0A263 THR 276 DELETION SEQADV 3UPG A UNP P0A263 SER 277 DELETION SEQADV 3UPG A UNP P0A263 TYR 278 DELETION SEQRES 1 A 338 ALA GLU ILE TYR ASN LYS ASP GLY ASN LYS LEU ASP LEU SEQRES 2 A 338 PHE GLY LYS VAL ASP GLY LEU HIS TYR PHE SER ASP ASP SEQRES 3 A 338 LYS GLY SER ASP GLY ASP GLN THR TYR MET ARG ILE GLY SEQRES 4 A 338 PHE LYS GLY GLU THR GLN VAL ASN ASP GLN LEU THR GLY SEQRES 5 A 338 TYR GLY GLN TRP GLU TYR GLN ILE GLN GLY ASN GLN THR SEQRES 6 A 338 GLU GLY SER ASN ASP SER TRP THR ARG VAL ALA PHE ALA SEQRES 7 A 338 GLY LEU LYS PHE ALA ASP ALA GLY SER PHE ASP TYR GLY SEQRES 8 A 338 ARG ASN TYR GLY VAL THR TYR ASP VAL THR SER TRP THR SEQRES 9 A 338 ASP VAL LEU PRO GLU PHE GLY GLY ASP THR TYR GLY ALA SEQRES 10 A 338 ASP ASN PHE MET GLN GLN ARG GLY ASN GLY TYR ALA THR SEQRES 11 A 338 TYR ARG ASN THR ASP PHE PHE GLY LEU VAL ASP GLY LEU SEQRES 12 A 338 ASP PHE ALA LEU GLN TYR GLN GLY LYS ASN GLY SER LEU SEQRES 13 A 338 LEU ASN GLN ASN GLY ASP GLY TYR GLY GLY SER LEU THR SEQRES 14 A 338 TYR ALA ILE GLY GLU GLY PHE SER VAL GLY GLY ALA ILE SEQRES 15 A 338 THR THR SER LYS ARG THR ALA ASP GLN ASN ASN THR ALA SEQRES 16 A 338 ASN ALA ARG LEU TYR GLY ASN GLY ASP ARG ALA THR VAL SEQRES 17 A 338 TYR THR GLY GLY LEU LYS TYR ASP ALA ASN ASN ILE TYR SEQRES 18 A 338 LEU ALA ALA GLN TYR SER GLN THR TYR ASN ALA THR ARG SEQRES 19 A 338 PHE GLY THR SER GLY PHE ALA ASN LYS ALA GLN ASN PHE SEQRES 20 A 338 GLU VAL VAL ALA GLN TYR GLN PHE ASP PHE GLY LEU ARG SEQRES 21 A 338 PRO SER VAL ALA TYR LEU GLN SER LYS GLY LYS ASP ILE SEQRES 22 A 338 SER ASN GLY TYR GLY ALA SER TYR GLY ASP GLN ASP ILE SEQRES 23 A 338 VAL LYS TYR VAL ASP VAL GLY ALA THR TYR TYR PHE ASN SEQRES 24 A 338 LYS ASN MET SER THR TYR VAL ASP TYR LYS ILE ASN LEU SEQRES 25 A 338 LEU ASP LYS ASN ASP PHE THR ARG ASP ALA GLY ILE ASN SEQRES 26 A 338 THR ASP ASP ILE VAL ALA LEU GLY LEU VAL TYR GLN PHE HET CA A 401 1 HET CA A 402 1 HET CL A 403 1 HET CL A 404 1 HET CL A 405 1 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 2 CA 2(CA 2+) FORMUL 4 CL 3(CL 1-) FORMUL 7 HOH *38(H2 O) HELIX 1 1 THR A 97 SER A 102 1 6 HELIX 2 2 TRP A 103 ASP A 105 5 3 HELIX 3 3 ASN A 316 ALA A 322 1 7 SHEET 1 A 5 GLU A 2 LYS A 6 0 SHEET 2 A 5 ASN A 9 ASP A 12 -1 O LEU A 11 N ILE A 3 SHEET 3 A 5 TYR A 35 GLN A 45 -1 O LYS A 41 N ASP A 12 SHEET 4 A 5 GLY A 15 PHE A 23 -1 N LYS A 16 O ARG A 37 SHEET 5 A 5 GLY A 31 ASP A 32 -1 O GLY A 31 N TYR A 22 SHEET 1 B19 GLU A 2 LYS A 6 0 SHEET 2 B19 ASN A 9 ASP A 12 -1 O LEU A 11 N ILE A 3 SHEET 3 B19 TYR A 35 GLN A 45 -1 O LYS A 41 N ASP A 12 SHEET 4 B19 LEU A 50 GLN A 61 -1 O TYR A 58 N ILE A 38 SHEET 5 B19 SER A 71 PHE A 82 -1 O ARG A 74 N GLU A 57 SHEET 6 B19 SER A 87 ARG A 92 -1 O ARG A 92 N ALA A 76 SHEET 7 B19 ALA A 129 ASN A 133 -1 O ARG A 132 N SER A 87 SHEET 8 B19 LEU A 143 GLN A 150 -1 O PHE A 145 N ASN A 133 SHEET 9 B19 GLY A 163 TYR A 170 -1 O SER A 167 N ALA A 146 SHEET 10 B19 PHE A 176 THR A 184 -1 O GLY A 180 N LEU A 168 SHEET 11 B19 THR A 207 ALA A 217 -1 O VAL A 208 N THR A 183 SHEET 12 B19 ILE A 220 GLN A 228 -1 O GLN A 228 N TYR A 209 SHEET 13 B19 GLN A 245 TYR A 253 -1 O GLU A 248 N GLN A 225 SHEET 14 B19 ARG A 260 LYS A 269 -1 O TYR A 265 N VAL A 249 SHEET 15 B19 ASP A 285 ASN A 299 -1 O GLY A 293 N SER A 262 SHEET 16 B19 MET A 302 ASN A 311 -1 O THR A 304 N TYR A 296 SHEET 17 B19 ILE A 329 TYR A 336 -1 O ILE A 329 N LYS A 309 SHEET 18 B19 GLY A 15 PHE A 23 -1 N GLY A 19 O LEU A 334 SHEET 19 B19 GLY A 31 ASP A 32 -1 O GLY A 31 N TYR A 22 LINK OD1 ASP A 135 CA CA A 401 1555 1555 2.76 LINK OD1 ASP A 328 CA CA A 402 1555 1555 3.19 LINK CA CA A 401 O HOH A 637 1555 1555 2.17 LINK CA CA A 401 O HOH A 638 1555 1555 2.19 LINK CA CA A 402 O HOH A 635 1555 1555 2.65 LINK CA CA A 402 O HOH A 636 1555 1555 1.96 SITE 1 AC1 4 ASP A 135 ASP A 144 HOH A 637 HOH A 638 SITE 1 AC2 5 ASN A 311 THR A 326 ASP A 328 HOH A 635 SITE 2 AC2 5 HOH A 636 SITE 1 AC3 2 THR A 114 ASN A 119 SITE 1 AC4 5 ARG A 37 GLN A 59 TRP A 72 ARG A 74 SITE 2 AC4 5 ARG A 124 SITE 1 AC5 1 ASN A 69 CRYST1 115.149 115.149 216.736 90.00 90.00 120.00 P 63 2 2 12 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 0.008684 0.005014 0.000000 0.00000 SCALE2 0.000000 0.010028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004614 0.00000