HEADER MEMBRANE PROTEIN 21-SEP-12 3VY9 TITLE CRYSTAL STRUCTURE OF PORB FROM NEISSERIA MENINGITIDIS IN COMPLEX WITH TITLE 2 CESIUM ION, SPACE GROUP H32 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN; 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 STRAIN: W135; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS BETA-BARREL, PORIN, CHANNEL, OUTER MEMBRANE PROTEIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.KATTNER,J.ZAUCHA,F.JAENECKE,U.ZACHARIAE,M.TANABE REVDAT 3 08-NOV-23 3VY9 1 REMARK LINK REVDAT 2 09-OCT-13 3VY9 1 JRNL REVDAT 1 02-JAN-13 3VY9 0 JRNL AUTH C.KATTNER,J.ZAUCHA,F.JAENECKE,U.ZACHARIAE,M.TANABE JRNL TITL IDENTIFICATION OF A CATION TRANSPORT PATHWAY IN NEISSERIA JRNL TITL 2 MENINGITIDIS PORB. JRNL REF PROTEINS V. 81 830 2013 JRNL REFN ISSN 0887-3585 JRNL PMID 23255122 JRNL DOI 10.1002/PROT.24241 REMARK 2 REMARK 2 RESOLUTION. 2.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 10.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 10770 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 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) : 2.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 599 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3420 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 : 4 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.03000 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): 1.832 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.385 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 : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.845 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2642 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3562 ; 1.908 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 7.692 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;35.307 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 431 ;24.153 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;22.638 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 374 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2047 ; 0.008 ; 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 3VY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000095650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-11 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 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 : 11968 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.630 REMARK 200 RESOLUTION RANGE LOW (A) : 81.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.860 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.3 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 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: 3A2R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% JEFFAMINE M600, 50MM CSCL, 0.1M REMARK 280 MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 72.10400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.62926 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.47033 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 72.10400 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 41.62926 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 35.47033 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 72.10400 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 41.62926 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 35.47033 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 72.10400 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 41.62926 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 35.47033 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 72.10400 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 41.62926 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 35.47033 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 72.10400 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 41.62926 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 35.47033 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 83.25853 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 70.94067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 83.25853 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 70.94067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 83.25853 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 70.94067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 83.25853 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 70.94067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 83.25853 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 70.94067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 83.25853 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 70.94067 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -409.0 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 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 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 501 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 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 ND2 ASN X 198 OE1 GLU X 202 1.94 REMARK 500 ND2 ASN X 244 CG2 ILE X 250 1.99 REMARK 500 OH TYR X 239 OE2 GLU X 256 2.12 REMARK 500 CG2 ILE X 250 OD1 ASN X 286 2.18 REMARK 500 NE ARG X 153 O HOH X 509 2.18 REMARK 500 NE2 GLN X 257 O TYR X 293 2.19 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 OE1 GLU X 49 OG1 THR X 310 2555 2.07 REMARK 500 CD1 ILE X 81 CD2 LEU X 337 2555 2.13 REMARK 500 OE2 GLU X 49 CD ARG X 309 2555 2.16 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 SER X 30 CB SER X 30 OG 0.079 REMARK 500 HIS X 164 CG HIS X 164 CD2 0.059 REMARK 500 TRP X 318 CE2 TRP X 318 CD2 0.073 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS X 323 CB - CA - C ANGL. DEV. = 17.6 DEGREES REMARK 500 LYS X 327 N - CA - CB ANGL. DEV. = 15.7 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 GLN X 26 118.52 -37.67 REMARK 500 ASN X 207 -1.19 83.74 REMARK 500 ASN X 210 -8.75 79.37 REMARK 500 LYS X 251 131.03 -38.04 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 CS X 403 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP X 109 O REMARK 620 2 GLU X 110 OE1 76.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS X 401 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY X 125 O REMARK 620 2 GLU X 128 O 72.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS X 402 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG X 130 O REMARK 620 2 GLU X 131 OE2 71.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS X 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS X 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS X 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS X 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VY8 RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH CESIUM IN DIFFERENT SPACE GROUP REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY REMARK 999 EXIST. DBREF 3VY9 X -13 341 PDB 3VY9 3VY9 -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 HET CS X 401 1 HET CS X 402 1 HET CS X 403 1 HET CS X 404 1 HETNAM CS CESIUM ION FORMUL 2 CS 4(CS 1+) FORMUL 6 HOH *12(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 THR X 123 GLU X 128 5 6 HELIX 6 6 PRO X 152 ASN X 157 1 6 HELIX 7 7 ASP X 158 LYS X 161 5 4 HELIX 8 8 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 LYS X 327 PHE X 341 -1 O PHE X 341 N GLY X 6 SHEET 4 A18 THR X 310 GLY X 322 -1 N GLY X 317 O ALA X 332 SHEET 5 A18 TYR X 295 ASP X 305 -1 N ASP X 296 O LYS X 320 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 TYR X 232 O ALA X 265 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 LEU X 197 O HIS X 212 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 VAL X 134 O TYR X 150 SHEET 14 A18 GLY X 88 ASN X 96 -1 N ARG X 91 O ARG X 135 SHEET 15 A18 ARG X 77 GLY X 85 -1 N GLY X 85 O GLY X 88 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 TYR X 5 O GLY X 44 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 LINK O TRP X 109 CS CS X 403 1555 1555 2.78 LINK OE1 GLU X 110 CS CS X 403 1555 1555 3.29 LINK O GLY X 125 CS CS X 401 1555 1555 3.11 LINK O GLU X 128 CS CS X 401 1555 1555 3.17 LINK O ARG X 130 CS CS X 402 1555 1555 2.80 LINK OE2 GLU X 131 CS CS X 402 1555 1555 2.54 SITE 1 AC1 2 GLY X 125 GLU X 128 SITE 1 AC2 2 ARG X 130 GLU X 131 SITE 1 AC3 2 TRP X 109 GLU X 110 SITE 1 AC4 1 ASN X 114 CRYST1 144.208 144.208 106.411 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 0.006934 0.004004 0.000000 0.00000 SCALE2 0.000000 0.008007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009398 0.00000