HEADER TRANSPORT PROTEIN 19-SEP-01 1K0F TITLE CRYSTAL STRUCTURE OF ZN(II)-FREE T. PALLIDUM TROA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC ZINC-BINDING PROTEIN TROA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TROMP-1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TREPONEMA PALLIDUM; SOURCE 3 ORGANISM_TAXID: 160; SOURCE 4 GENE: TROA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5A; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX1 KEYWDS APO PROTEIN, HELIX BACKBONE, CLOSED CONFORMATION, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.LEE,M.R.DORWART,K.R.HAZLETT,R.K.DEKA,M.V.NORGARD,J.D.RADOLF, AUTHOR 2 C.A.HASEMANN REVDAT 4 16-AUG-23 1K0F 1 REMARK REVDAT 3 24-FEB-09 1K0F 1 VERSN REVDAT 2 29-APR-03 1K0F 1 REMARK REVDAT 1 10-APR-02 1K0F 0 JRNL AUTH Y.H.LEE,M.R.DORWART,K.R.HAZLETT,R.K.DEKA,M.V.NORGARD, JRNL AUTH 2 J.D.RADOLF,C.A.HASEMANN JRNL TITL THE CRYSTAL STRUCTURE OF ZN(II)-FREE TREPONEMA PALLIDUM JRNL TITL 2 TROA, A PERIPLASMIC METAL-BINDING PROTEIN, REVEALS A CLOSED JRNL TITL 3 CONFORMATION. JRNL REF J.BACTERIOL. V. 184 2300 2002 JRNL REFN ISSN 0021-9193 JRNL PMID 11914363 JRNL DOI 10.1128/JB.184.8.2300-2304.2002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.H.LEE,R.K.DEKA,M.V.NORGARD,J.D.RADOLF,C.A.HASEMANN REMARK 1 TITL TREPONEMA PALLIDUM TROA IS A PERIPLASMIC ZINC-BINDING REMARK 1 TITL 2 PROTEIN WITH A HELICAL BACKBONE REMARK 1 REF NAT.STRUCT.BIOL. V. 6 628 1999 REMARK 1 REFN ISSN 1072-8368 REMARK 1 DOI 10.1038/10677 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13646 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 SET) : 0.208 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2138 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE FACTOR FILE FOR THIS ENTRY HAS BEEN REMOVED REMARK 3 FROM THE ARCHIVE BECAUSE IT WAS FOUND TO BE REMARK 3 INCOMPLETE. REMARK 4 REMARK 4 1K0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC CONFOCAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13646 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1TOA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG2000, PH 4.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 58.68000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.68000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.17500 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 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: 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 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 O HOH A 327 O HOH A 327 2655 2.04 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 THR A 39 -92.39 -91.31 REMARK 500 GLN A 52 -128.50 56.99 REMARK 500 PRO A 63 152.54 -43.36 REMARK 500 LEU A 69 33.82 -92.72 REMARK 500 THR A 73 -175.12 -61.64 REMARK 500 ASN A 89 -72.83 -51.55 REMARK 500 GLU A 94 44.95 -75.05 REMARK 500 THR A 95 -51.05 -21.02 REMARK 500 LYS A 96 36.14 -86.59 REMARK 500 GLU A 115 12.53 -69.67 REMARK 500 PRO A 118 106.65 -43.75 REMARK 500 VAL A 119 -37.16 -27.34 REMARK 500 GLU A 127 -13.39 63.33 REMARK 500 ALA A 169 -70.84 -49.21 REMARK 500 ASP A 200 68.25 -63.15 REMARK 500 PHE A 202 21.13 -140.66 REMARK 500 SER A 223 114.33 -168.26 REMARK 500 GLU A 224 -176.15 -69.91 REMARK 500 LYS A 254 -21.26 -37.68 REMARK 500 ALA A 265 2.89 -69.31 REMARK 500 SER A 278 -81.20 -94.82 REMARK 500 ASP A 300 -70.35 -59.26 REMARK 500 ALA A 305 6.30 -66.06 REMARK 500 ALA A 307 -148.16 -85.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TOA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZN(II)-BOUND T. PALLIDUM TROA DBREF 1K0F A 32 308 UNP P96116 TROA_TREPA 32 308 SEQRES 1 A 277 GLY LYS PRO LEU VAL VAL THR THR ILE GLY MET ILE ALA SEQRES 2 A 277 ASP ALA VAL LYS ASN ILE ALA GLN GLY ASP VAL HIS LEU SEQRES 3 A 277 LYS GLY LEU MET GLY PRO GLY VAL ASP PRO HIS LEU TYR SEQRES 4 A 277 THR ALA THR ALA GLY ASP VAL GLU TRP LEU GLY ASN ALA SEQRES 5 A 277 ASP LEU ILE LEU TYR ASN GLY LEU HIS LEU GLU THR LYS SEQRES 6 A 277 MET GLY GLU VAL PHE SER LYS LEU ARG GLY SER ARG LEU SEQRES 7 A 277 VAL VAL ALA VAL SER GLU THR ILE PRO VAL SER GLN ARG SEQRES 8 A 277 LEU SER LEU GLU GLU ALA GLU PHE ASP PRO HIS VAL TRP SEQRES 9 A 277 PHE ASP VAL LYS LEU TRP SER TYR SER VAL LYS ALA VAL SEQRES 10 A 277 TYR GLU SER LEU CYS LYS LEU LEU PRO GLY LYS THR ARG SEQRES 11 A 277 GLU PHE THR GLN ARG TYR GLN ALA TYR GLN GLN GLN LEU SEQRES 12 A 277 ASP LYS LEU ASP ALA TYR VAL ARG ARG LYS ALA GLN SER SEQRES 13 A 277 LEU PRO ALA GLU ARG ARG VAL LEU VAL THR ALA HIS ASP SEQRES 14 A 277 ALA PHE GLY TYR PHE SER ARG ALA TYR GLY PHE GLU VAL SEQRES 15 A 277 LYS GLY LEU GLN GLY VAL SER THR ALA SER GLU ALA SER SEQRES 16 A 277 ALA HIS ASP MET GLN GLU LEU ALA ALA PHE ILE ALA GLN SEQRES 17 A 277 ARG LYS LEU PRO ALA ILE PHE ILE GLU SER SER ILE PRO SEQRES 18 A 277 HIS LYS ASN VAL GLU ALA LEU ARG ASP ALA VAL GLN ALA SEQRES 19 A 277 ARG GLY HIS VAL VAL GLN ILE GLY GLY GLU LEU PHE SER SEQRES 20 A 277 ASP ALA MET GLY ASP ALA GLY THR SER GLU GLY THR TYR SEQRES 21 A 277 VAL GLY MET VAL THR HIS ASN ILE ASP THR ILE VAL ALA SEQRES 22 A 277 ALA LEU ALA ARG FORMUL 2 HOH *28(H2 O) HELIX 1 1 GLY A 41 GLN A 52 1 12 HELIX 2 2 GLY A 53 VAL A 55 5 3 HELIX 3 3 THR A 73 ALA A 83 1 11 HELIX 4 4 GLU A 94 LYS A 96 5 3 HELIX 5 5 MET A 97 ARG A 105 1 9 HELIX 6 6 SER A 114 ILE A 117 5 4 HELIX 7 7 PRO A 118 ARG A 122 5 5 HELIX 8 8 HIS A 133 PHE A 136 5 4 HELIX 9 9 ASP A 137 LEU A 156 1 20 HELIX 10 10 LYS A 159 LEU A 188 1 30 HELIX 11 11 PRO A 189 ARG A 192 5 4 HELIX 12 12 PHE A 202 GLY A 210 1 9 HELIX 13 13 SER A 226 ARG A 240 1 15 HELIX 14 14 PRO A 252 LYS A 254 5 3 HELIX 15 15 ASN A 255 ALA A 265 1 11 HELIX 16 16 THR A 290 ALA A 305 1 16 SHEET 1 A 4 HIS A 56 MET A 61 0 SHEET 2 A 4 LEU A 35 ILE A 40 1 N THR A 38 O LEU A 60 SHEET 3 A 4 LEU A 85 TYR A 88 1 O LEU A 85 N VAL A 37 SHEET 4 A 4 LEU A 109 ALA A 112 1 O LEU A 109 N ILE A 86 SHEET 1 B 2 SER A 124 LEU A 125 0 SHEET 2 B 2 GLU A 129 PHE A 130 -1 O GLU A 129 N LEU A 125 SHEET 1 C 2 VAL A 194 HIS A 199 0 SHEET 2 C 2 GLU A 212 GLN A 217 1 O LEU A 216 N THR A 197 SHEET 1 D 2 ALA A 244 GLU A 248 0 SHEET 2 D 2 GLN A 271 LEU A 276 1 O LEU A 276 N ILE A 247 CRYST1 117.360 38.350 104.470 90.00 104.11 90.00 C 1 2 1 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 0.008521 0.000000 0.002142 0.00000 SCALE2 0.000000 0.026076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009870 0.00000