HEADER MEMBRANE PROTEIN 28-DEC-05 2FI9 TITLE THE CRYSTAL STRUCTURE OF AN OUTER MEMBRANE PROTEIN FROM THE BARTONELLA TITLE 2 HENSELAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BARTONELLA HENSELAE; SOURCE 3 ORGANISM_TAXID: 283166; SOURCE 4 STRAIN: STR. HOUSTON-1; SOURCE 5 GENE: GI:49238164; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDM68 KEYWDS STRUCTURAL GENOMICS,OUTER MEMBRANE PROTEIN, BARTONELLA HENSELAE, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, MCSG, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,C.HATZOS,S.CLANCY,F.COLLART,M.CYMBOROWSKI,W.MINOR, AUTHOR 2 A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 3 13-JUL-11 2FI9 1 VERSN REVDAT 2 24-FEB-09 2FI9 1 VERSN REVDAT 1 14-FEB-06 2FI9 0 JRNL AUTH R.ZHANG,C.HATZOS,S.CLANCY,F.COLLART,M.CYMBOROWSKI,W.MINOR, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL THE 1.8A CRYSTAL STRUCTURE OF AN OUTER MEMBRANE PROTEIN FROM JRNL TITL 2 THE BARTONELLA HENSELAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 8970 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 447 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 292 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 39.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 15 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 905 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 35.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.51000 REMARK 3 B22 (A**2) : 1.20000 REMARK 3 B33 (A**2) : -0.69000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.244 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 921 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1250 ; 1.325 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 117 ; 5.766 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 40 ;24.705 ;23.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 153 ;13.286 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.855 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 145 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 698 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 433 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 662 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 48 ; 0.152 ; 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): 45 ; 0.191 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.130 ; 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): 601 ; 0.689 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 943 ; 1.146 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 354 ; 2.023 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 307 ; 3.319 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 50 REMARK 3 RESIDUE RANGE : A 51 A 90 REMARK 3 RESIDUE RANGE : A 91 A 128 REMARK 3 ORIGIN FOR THE GROUP (A): 23.0700 32.3670 23.6350 REMARK 3 T TENSOR REMARK 3 T11: 0.1491 T22: -0.1013 REMARK 3 T33: -0.2427 T12: -0.0062 REMARK 3 T13: 0.0054 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 1.7943 L22: 1.7642 REMARK 3 L33: 4.1723 L12: -0.5447 REMARK 3 L13: 0.9432 L23: -0.1071 REMARK 3 S TENSOR REMARK 3 S11: 0.0398 S12: 0.0247 S13: 0.0166 REMARK 3 S21: -0.0698 S22: -0.0049 S23: 0.0106 REMARK 3 S31: 0.2253 S32: 0.0171 S33: -0.0348 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2FI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-06. REMARK 100 THE RCSB ID CODE IS RCSB035909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SBCCOLLECT REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8970 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 35.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M (NH4)2SO4, 0.1M CAPS PH10.5, 0.2M REMARK 280 LI2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 17.26350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.18400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.96550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.18400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.26350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.96550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THIS REMARK 300 MOLECULE IS UNKNOWN. 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: 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 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 SER A 2 REMARK 465 HIS A 3 REMARK 465 ALA A 4 REMARK 465 ILE A 5 REMARK 465 GLN A 6 REMARK 465 ILE A 7 REMARK 465 ARG A 8 REMARK 465 GLU A 9 REMARK 465 ALA A 10 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 PHE A 12 133.04 177.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC84470 RELATED DB: TARGETDB DBREF 2FI9 A 1 128 GB 49238164 CAF27373 1 128 SEQRES 1 A 128 MET SER HIS ALA ILE GLN ILE ARG GLU ALA HIS PHE PRO SEQRES 2 A 128 GLY ARG ALA PRO ILE ASP ALA TYR GLY ASN GLY GLY PHE SEQRES 3 A 128 ARG PHE ALA ASP MET SER HIS ARG GLY SER ILE ILE CYS SEQRES 4 A 128 ILE PRO SER GLY ILE TYR GLY ILE ASP MET THR GLY PRO SEQRES 5 A 128 VAL PRO THR GLN GLU ASP ILE SER ARG VAL LEU GLU GLU SEQRES 6 A 128 SER ASP GLN ILE GLU VAL LEU LEU ILE GLY THR GLY VAL SEQRES 7 A 128 GLU LEU LEU ARG LEU PRO GLU GLU LEU ARG VAL LEU LEU SEQRES 8 A 128 TRP GLU LYS ARG ILE SER SER ASP THR MET SER THR GLY SEQRES 9 A 128 ALA ALA VAL ARG THR PHE ASN VAL LEU LEU ALA GLU ASP SEQRES 10 A 128 ARG ALA VAL ALA ALA LEU LEU PHE ALA VAL GLU FORMUL 2 HOH *53(H2 O) HELIX 1 1 GLN A 56 ASP A 58 5 3 HELIX 2 2 ILE A 59 GLU A 65 1 7 HELIX 3 3 SER A 66 ILE A 69 5 4 HELIX 4 4 PRO A 84 LYS A 94 1 11 HELIX 5 5 SER A 102 GLU A 116 1 15 SHEET 1 A 3 ILE A 18 GLY A 22 0 SHEET 2 A 3 GLY A 25 PHE A 28 -1 O ARG A 27 N ALA A 20 SHEET 3 A 3 MET A 31 ARG A 34 -1 O HIS A 33 N PHE A 26 SHEET 1 B 5 GLY A 43 ILE A 47 0 SHEET 2 B 5 SER A 36 ILE A 40 -1 N ILE A 40 O GLY A 43 SHEET 3 B 5 VAL A 120 LEU A 124 -1 O LEU A 124 N ILE A 37 SHEET 4 B 5 VAL A 71 GLY A 75 1 N GLY A 75 O LEU A 123 SHEET 5 B 5 SER A 97 MET A 101 1 O SER A 97 N LEU A 72 CRYST1 34.527 51.931 62.368 90.00 90.00 90.00 P 21 21 21 4 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 0.028963 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016034 0.00000 MASTER 286 0 0 5 8 0 0 6 0 0 0 10 END