HEADER TRANSPORT PROTEIN 13-AUG-11 3TEF TITLE CRYSTAL STRUCTURE OF THE PERIPLASMIC CATECHOLATE-SIDEROPHORE BINDING TITLE 2 PROTEIN VCTP FROM VIBRIO CHOLERAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON(III) ABC TRANSPORTER, PERIPLASMIC IRON-COMPOUND- COMPND 3 BINDING PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 51-333; COMPND 6 SYNONYM: VCTP; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: VC_A0227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIDEROPHORE-BINDING PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.LIU,Z.WANG,S.LIU,N.LI,Y.CHEN,C.ZHU,D.ZHU,T.WEI,Y.HUANG,S.XU,L.GU REVDAT 2 20-MAR-24 3TEF 1 SEQADV REVDAT 1 15-AUG-12 3TEF 0 JRNL AUTH X.LIU,Q.DU,Z.WANG,S.LIU,N.LI,Y.CHEN,C.ZHU,D.ZHU,T.WEI, JRNL AUTH 2 Y.HUANG,S.XU,L.GU JRNL TITL CRYSTAL STRUCTURE OF PERIPLASMIC CATECHOLATE-SIDEROPHORE JRNL TITL 2 BINDING PROTEIN VCTP FROM VIBRIO CHOLERAE AT 1.7 A JRNL TITL 3 RESOLUTION JRNL REF FEBS LETT. V. 586 1240 2012 JRNL REFN ISSN 0014-5793 JRNL PMID 22575663 JRNL DOI 10.1016/J.FEBSLET.2012.03.043 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 29042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.650 REMARK 3 FREE R VALUE TEST SET COUNT : 1932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.4645 - 4.0898 0.98 2151 153 0.1902 0.1715 REMARK 3 2 4.0898 - 3.2471 1.00 2075 147 0.1663 0.1945 REMARK 3 3 3.2471 - 2.8369 1.00 2061 146 0.2005 0.2613 REMARK 3 4 2.8369 - 2.5776 1.00 2013 144 0.1959 0.2455 REMARK 3 5 2.5776 - 2.3929 0.99 2013 142 0.1989 0.2118 REMARK 3 6 2.3929 - 2.2519 0.99 1998 139 0.1858 0.1871 REMARK 3 7 2.2519 - 2.1391 0.99 1960 139 0.1905 0.2348 REMARK 3 8 2.1391 - 2.0460 0.98 1967 140 0.1882 0.2068 REMARK 3 9 2.0460 - 1.9673 0.97 1955 138 0.1865 0.2016 REMARK 3 10 1.9673 - 1.8994 0.95 1849 130 0.1953 0.2601 REMARK 3 11 1.8994 - 1.8400 0.93 1874 136 0.1994 0.2646 REMARK 3 12 1.8400 - 1.7874 0.91 1784 132 0.2101 0.2666 REMARK 3 13 1.7874 - 1.7403 0.89 1786 128 0.2471 0.3247 REMARK 3 14 1.7403 - 1.6979 0.82 1624 118 0.2750 0.3315 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 40.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.40420 REMARK 3 B22 (A**2) : 11.83170 REMARK 3 B33 (A**2) : -2.42760 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2232 REMARK 3 ANGLE : 0.978 3024 REMARK 3 CHIRALITY : 0.071 338 REMARK 3 PLANARITY : 0.004 390 REMARK 3 DIHEDRAL : 13.244 817 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3TEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067379. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30253 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.698 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.59700 REMARK 200 R SYM FOR SHELL (I) : 0.59700 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL REMARK 280 BUFFER, 20% PEG3350, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 16.05600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.40950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.64100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.40950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.05600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.64100 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 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 MET A 50 REMARK 465 VAL A 330 REMARK 465 GLY A 331 REMARK 465 MET A 332 REMARK 465 GLN A 333 REMARK 465 LEU A 334 REMARK 465 GLU A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 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 HOH A 441 O HOH A 473 1.90 REMARK 500 O HOH A 359 O HOH A 430 1.97 REMARK 500 O HOH A 428 O HOH A 459 2.16 REMARK 500 N HIS A 248 O HOH A 427 2.16 REMARK 500 ND1 HIS A 248 O HOH A 427 2.17 REMARK 500 O HOH A 49 O HOH A 396 2.19 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 LYS A 205 109.27 -43.74 REMARK 500 ASN A 224 43.16 -104.00 REMARK 500 SER A 243 -143.70 39.79 REMARK 500 ILE A 252 -156.95 -128.29 REMARK 500 ALA A 312 58.86 -93.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 3TEF A 51 333 UNP Q9KMU2 Q9KMU2_VIBCH 51 333 SEQADV 3TEF MET A 50 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF LEU A 334 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF GLU A 335 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF HIS A 336 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF HIS A 337 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF HIS A 338 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF HIS A 339 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF HIS A 340 UNP Q9KMU2 EXPRESSION TAG SEQADV 3TEF HIS A 341 UNP Q9KMU2 EXPRESSION TAG SEQRES 1 A 292 MET GLU THR VAL THR ILE GLU HIS ARG LEU GLY LYS THR SEQRES 2 A 292 THR LEU GLU GLN LYS PRO GLN ARG VAL VAL VAL ILE GLY SEQRES 3 A 292 VAL GLY ALA LEU ASP ALA ILE ASP SER PHE GLY ILE GLU SEQRES 4 A 292 PRO VAL ALA VAL SER LYS PHE ASP GLY THR PRO ASP TYR SEQRES 5 A 292 LEU ALA LYS TYR LYS SER ASP LYS TYR PRO SER ALA GLY SEQRES 6 A 292 SER LEU PHE GLU PRO ASP PHE GLU THR ILE TYR THR GLN SEQRES 7 A 292 LYS PRO ASP LEU ILE VAL ILE GLY PRO ARG ALA SER LYS SEQRES 8 A 292 SER TYR ASP GLU LEU SER LYS ILE ALA PRO THR ILE VAL SEQRES 9 A 292 PHE ALA ALA GLU ALA ASP GLN GLY TYR TRP GLU SER THR SEQRES 10 A 292 GLN GLN GLN TRP ARG ASN LEU GLY LYS VAL PHE ALA ILE SEQRES 11 A 292 GLU PRO ALA VAL GLU ALA LYS ILE GLU GLN VAL ASP ALA SEQRES 12 A 292 GLN PHE LYS SER ILE MET GLN TYR ASN GLN GLN HIS LYS SEQRES 13 A 292 SER ASP ALA MET LEU VAL MET SER SER GLY GLY ASN LEU SEQRES 14 A 292 THR THR PHE GLY ALA ASN SER ARG PHE SER SER VAL TYR SEQRES 15 A 292 LYS ASP PHE GLY PHE SER GLU THR VAL PRO VAL SER LYS SEQRES 16 A 292 GLU SER SER HIS GLY ASP LEU ILE SER PHE GLU TYR ILE SEQRES 17 A 292 ARG GLU HIS ASN PRO LYS THR LEU LEU VAL VAL ASP ARG SEQRES 18 A 292 ASP LYS VAL VAL THR LYS GLY GLU THR ASN ILE ARG GLN SEQRES 19 A 292 THR PHE GLU ASN ASP LEU VAL LYS ALA THR THR ALA TYR SEQRES 20 A 292 LYS ASN GLY HIS ILE ALA TYR LEU ASP VAL ASN ALA TRP SEQRES 21 A 292 TYR ILE ALA ILE SER GLY VAL LYS ALA THR GLU GLN MET SEQRES 22 A 292 VAL ALA ASP MET LYS ALA SER VAL GLY MET GLN LEU GLU SEQRES 23 A 292 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *182(H2 O) HELIX 1 1 GLY A 75 PHE A 85 1 11 HELIX 2 2 PRO A 99 SER A 107 5 9 HELIX 3 3 ASP A 120 GLN A 127 1 8 HELIX 4 4 PRO A 136 LYS A 140 5 5 HELIX 5 5 SER A 141 ALA A 149 1 9 HELIX 6 6 GLY A 161 ALA A 178 1 18 HELIX 7 7 ILE A 179 HIS A 204 1 26 HELIX 8 8 SER A 228 ASP A 233 1 6 HELIX 9 9 SER A 253 ASN A 261 1 9 HELIX 10 10 ARG A 270 THR A 275 1 6 HELIX 11 11 ASN A 280 GLU A 286 1 7 HELIX 12 12 ASN A 287 ALA A 292 1 6 HELIX 13 13 THR A 293 ASN A 298 1 6 HELIX 14 14 ASP A 305 TYR A 310 1 6 HELIX 15 15 GLY A 315 SER A 329 1 15 SHEET 1 A 2 THR A 52 HIS A 57 0 SHEET 2 A 2 GLY A 60 GLU A 65 -1 O GLY A 60 N HIS A 57 SHEET 1 B 4 ALA A 91 VAL A 92 0 SHEET 2 B 4 VAL A 71 ILE A 74 1 N VAL A 73 O ALA A 91 SHEET 3 B 4 LEU A 131 ILE A 134 1 O VAL A 133 N VAL A 72 SHEET 4 B 4 THR A 151 VAL A 153 1 O ILE A 152 N ILE A 134 SHEET 1 C 4 SER A 237 GLU A 238 0 SHEET 2 C 4 ASP A 207 SER A 214 1 N ALA A 208 O SER A 237 SHEET 3 C 4 ASN A 217 PHE A 221 -1 O THR A 219 N MET A 212 SHEET 4 C 4 ASP A 250 LEU A 251 -1 O ASP A 250 N THR A 220 SHEET 1 D 4 SER A 237 GLU A 238 0 SHEET 2 D 4 ASP A 207 SER A 214 1 N ALA A 208 O SER A 237 SHEET 3 D 4 THR A 264 ASP A 269 1 O LEU A 266 N VAL A 211 SHEET 4 D 4 ILE A 301 TYR A 303 1 O ALA A 302 N VAL A 267 CRYST1 32.112 73.282 112.819 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 0.031141 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008864 0.00000