HEADER MEMBRANE PROTEIN 18-OCT-04 1XS5 TITLE THE CRYSTAL STRUCTURE OF LIPOPROTEIN TP32 FROM TREPONEMA PALLIDUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEMBRANE LIPOPROTEIN TPN32; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 29 KDA PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TREPONEMA PALLIDUM; SOURCE 3 ORGANISM_TAXID: 160; SOURCE 4 GENE: TPN32; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL-1 BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX HTB-TP32 KEYWDS LIPOPROTEIN, PERIPLASMIC BINDING PROTEIN, METHIONINE, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.K.DEKA,L.NEIL,K.E.HAGMAN,M.MACHIUS,D.R.TOMCHICK,C.A.BRAUTIGAM, AUTHOR 2 M.V.NORGARD REVDAT 4 14-FEB-24 1XS5 1 REMARK REVDAT 3 24-FEB-09 1XS5 1 VERSN REVDAT 2 19-APR-05 1XS5 1 JRNL REVDAT 1 23-NOV-04 1XS5 0 JRNL AUTH R.K.DEKA,L.NEIL,K.E.HAGMAN,M.MACHIUS,D.R.TOMCHICK, JRNL AUTH 2 C.A.BRAUTIGAM,M.V.NORGARD JRNL TITL STRUCTURAL EVIDENCE THAT THE 32-KILODALTON LIPOPROTEIN JRNL TITL 2 (TP32) OF TREPONEMA PALLIDUM IS AN L-METHIONINE-BINDING JRNL TITL 3 PROTEIN JRNL REF J.BIOL.CHEM. V. 279 55644 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15489229 JRNL DOI 10.1074/JBC.M409263200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 594357.420 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 20386 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) : 0.183 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1417 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2585 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 183 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1854 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.36000 REMARK 3 B22 (A**2) : 6.73000 REMARK 3 B33 (A**2) : -3.37000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.130 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 35.93 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.PARAM REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XS5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.98 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR, SI REMARK 200 -220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 35.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58700 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SUCCINIC ACID, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 48.12400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.20200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.12400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.20200 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 300 REMARK: MONOMER CONTAINED IN ASYMMETRIC UNIT IS THE BIOLOGICAL UNIT. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 LEU A 245 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 ASN A 148 O HOH A 1163 2.14 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 SER A 15 -172.40 -173.87 REMARK 500 PHE A 61 -6.46 -161.70 REMARK 500 THR A 95 -42.49 -136.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MET A 301 DBREF 1XS5 A 5 245 UNP O07950 TPN32_TREPA 28 268 SEQRES 1 A 241 LYS ASP GLU THR VAL GLY VAL GLY VAL LEU SER GLU PRO SEQRES 2 A 241 HIS ALA ARG LEU LEU GLU ILE ALA LYS GLU GLU VAL LYS SEQRES 3 A 241 LYS GLN HIS ILE GLU LEU ARG ILE VAL GLU PHE THR ASN SEQRES 4 A 241 TYR VAL ALA LEU ASN GLU ALA VAL MET ARG GLY ASP ILE SEQRES 5 A 241 LEU MET ASN PHE PHE GLN HIS VAL PRO HIS MET GLN GLN SEQRES 6 A 241 PHE ASN GLN GLU HIS ASN GLY ASP LEU VAL SER VAL GLY SEQRES 7 A 241 ASN VAL HIS VAL GLU PRO LEU ALA LEU TYR SER ARG THR SEQRES 8 A 241 TYR ARG HIS VAL SER ASP PHE PRO ALA GLY ALA VAL ILE SEQRES 9 A 241 ALA ILE PRO ASN ASP SER SER ASN GLU ALA ARG ALA LEU SEQRES 10 A 241 ARG LEU LEU GLU ALA ALA GLY PHE ILE ARG MET ARG ALA SEQRES 11 A 241 GLY SER GLY LEU PHE ALA THR VAL GLU ASP VAL GLN GLN SEQRES 12 A 241 ASN VAL ARG ASN VAL VAL LEU GLN GLU VAL GLU SER ALA SEQRES 13 A 241 LEU LEU PRO ARG VAL PHE ASP GLN VAL ASP GLY ALA VAL SEQRES 14 A 241 ILE ASN GLY ASN TYR ALA ILE MET ALA GLY LEU SER ALA SEQRES 15 A 241 ARG ARG ASP GLY LEU ALA VAL GLU PRO ASP ALA SER ALA SEQRES 16 A 241 TYR ALA ASN VAL LEU VAL VAL LYS ARG GLY ASN GLU ALA SEQRES 17 A 241 ASP ALA ARG VAL GLN ALA VAL LEU ARG ALA LEU CYS GLY SEQRES 18 A 241 GLY ARG VAL ARG THR TYR LEU LYS GLU ARG TYR LYS GLY SEQRES 19 A 241 GLY GLU VAL ALA PRO ALA LEU HET MET A 301 9 HETNAM MET METHIONINE FORMUL 2 MET C5 H11 N O2 S FORMUL 3 HOH *201(H2 O) HELIX 1 1 PRO A 17 LYS A 31 1 15 HELIX 2 2 ASN A 43 ARG A 53 1 11 HELIX 3 3 VAL A 64 ASN A 75 1 12 HELIX 4 4 HIS A 98 PHE A 102 5 5 HELIX 5 5 ASP A 113 ALA A 127 1 15 HELIX 6 6 THR A 141 GLU A 143 5 3 HELIX 7 7 GLU A 158 ALA A 160 5 3 HELIX 8 8 LEU A 161 PHE A 166 1 6 HELIX 9 9 ASP A 167 VAL A 169 5 3 HELIX 10 10 ASN A 175 ALA A 182 1 8 HELIX 11 11 ASP A 196 TYR A 200 5 5 HELIX 12 12 ASP A 213 CYS A 224 1 12 HELIX 13 13 GLY A 225 TYR A 236 1 12 SHEET 1 A 6 ILE A 34 GLU A 40 0 SHEET 2 A 6 GLU A 7 VAL A 13 1 N VAL A 9 O ARG A 37 SHEET 3 A 6 MET A 58 HIS A 63 1 O PHE A 60 N GLY A 12 SHEET 4 A 6 ASN A 202 LYS A 207 -1 O VAL A 203 N GLN A 62 SHEET 5 A 6 LEU A 78 VAL A 86 -1 N HIS A 85 O ASN A 202 SHEET 6 A 6 ALA A 242 PRO A 243 -1 O ALA A 242 N VAL A 86 SHEET 1 B 5 VAL A 153 VAL A 157 0 SHEET 2 B 5 VAL A 107 PRO A 111 1 N ILE A 108 O VAL A 153 SHEET 3 B 5 GLY A 171 ILE A 174 1 O VAL A 173 N ALA A 109 SHEET 4 B 5 ALA A 90 TYR A 92 -1 N TYR A 92 O ALA A 172 SHEET 5 B 5 ALA A 192 VAL A 193 -1 O ALA A 192 N LEU A 91 SHEET 1 C 2 ARG A 131 MET A 132 0 SHEET 2 C 2 VAL A 145 GLN A 147 -1 O GLN A 147 N ARG A 131 CISPEP 1 GLU A 16 PRO A 17 0 0.10 SITE 1 AC1 15 HIS A 18 TYR A 44 PHE A 61 GLN A 62 SITE 2 AC1 15 HIS A 63 HIS A 66 GLU A 87 ASN A 116 SITE 3 AC1 15 ARG A 119 ASN A 175 ASN A 177 ASN A 202 SITE 4 AC1 15 HOH A1004 HOH A1014 HOH A1038 CRYST1 96.248 46.404 55.217 90.00 90.00 90.00 P 21 21 2 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 0.010390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018110 0.00000