HEADER MEMBRANE PROTEIN 18-OCT-04 1XS5 TITLE THE CRYSTAL STRUCTURE OF LIPOPROTEIN TP32 FROM TREPONEMA TITLE 2 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, KEYWDS 2 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.K.DEKA,L.NEIL,K.E.HAGMAN,M.MACHIUS,D.R.TOMCHICK, AUTHOR 2 C.A.BRAUTIGAM,M.V.NORGARD 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 JRNL TITL 2 LIPOPROTEIN (TP32) OF TREPONEMA PALLIDUM IS AN JRNL TITL 3 L-METHIONINE-BINDING 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 1 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 : 1881 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 202 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) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.13 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. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-04. REMARK 100 THE RCSB ID CODE IS RCSB030704. 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, REMARK 200 SI-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 REMARK 300 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 MASTER 263 0 1 13 13 0 4 6 0 0 0 19 END