HEADER TRANSPORT PROTEIN 12-FEB-07 2OV1 TITLE CRYSTAL STRUCTURE OF APO FORM OF ZNUA WITH FLEXIBLE LOOP DELETION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC BINDING PROTEIN COMPONENT OF AN ABC TYPE ZINC COMPND 3 UPTAKE TRANSPORTER; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. (STRAIN PCC 6803 / KAZUSA); SOURCE 3 ORGANISM_TAXID: 1111708; SOURCE 4 STRAIN: PCC 6803 / KAZUSA; SOURCE 5 GENE: ZNTC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS ABC TRANSPORTER, ZINC TRANSPORTER, SOLUTE BINDING DOMAIN, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.J.SMITH,B.WEI REVDAT 5 30-AUG-23 2OV1 1 REMARK REVDAT 4 21-JUN-17 2OV1 1 SOURCE DBREF REVDAT 3 24-FEB-09 2OV1 1 VERSN REVDAT 2 20-NOV-07 2OV1 1 JRNL REVDAT 1 10-JUL-07 2OV1 0 JRNL AUTH B.WEI,A.M.RANDICH,M.BHATTACHARYYA-PAKRASI,H.B.PAKRASI, JRNL AUTH 2 T.J.SMITH JRNL TITL POSSIBLE REGULATORY ROLE FOR THE HISTIDINE-RICH LOOP IN THE JRNL TITL 2 ZINC TRANSPORT PROTEIN, ZNUA. JRNL REF BIOCHEMISTRY V. 46 8734 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17616151 JRNL DOI 10.1021/BI700763W REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 279.00 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 10189 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 5% REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 501 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 : 2020 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.64100 REMARK 3 B22 (A**2) : 6.56500 REMARK 3 B33 (A**2) : -11.20500 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) : 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.308 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.343 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.281 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.928 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.920 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 33.18 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08880 REMARK 200 FOR THE DATA SET : NULL 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) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28500 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1PQ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 63.57550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.57550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.28900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.25150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.28900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.25150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.57550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.28900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.25150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.57550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.28900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.25150 REMARK 290 SMTRY3 8 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: 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 ASN A 120 98.88 -166.68 REMARK 500 PRO A 267 121.04 -36.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PQ4 RELATED DB: PDB REMARK 900 FULL LENGTH ZNUA WITH ZINC BOUND DBREF 2OV1 A 47 137 UNP P73085 P73085_SYNY3 47 137 DBREF 2OV1 A 141 338 UNP P73085 P73085_SYNY3 173 338 SEQADV 2OV1 PRO A 138 UNP P73085 LINKER SEQADV 2OV1 GLY A 139 UNP P73085 LINKER SEQADV 2OV1 ARG A 140 UNP P73085 LINKER SEQRES 1 A 260 ASP ALA MET ASP ILE THR VAL SER ILE PRO PRO GLN GLN SEQRES 2 A 260 TYR PHE LEU GLU LYS ILE GLY GLY ASP LEU VAL ARG VAL SEQRES 3 A 260 SER VAL LEU VAL PRO GLY ASN ASN ASP PRO HIS THR TYR SEQRES 4 A 260 GLU PRO LYS PRO GLN GLN LEU ALA ALA LEU SER GLU ALA SEQRES 5 A 260 GLU ALA TYR VAL LEU ILE GLY LEU GLY PHE GLU GLN PRO SEQRES 6 A 260 TRP LEU GLU LYS LEU LYS ALA ALA ASN ALA ASN MET LYS SEQRES 7 A 260 LEU ILE ASP SER ALA GLN GLY ILE THR PRO LEU GLU MET SEQRES 8 A 260 PRO GLY ARG LEU MET VAL ALA ASP PRO HIS ILE TRP LEU SEQRES 9 A 260 SER PRO THR LEU VAL LYS ARG GLN ALA THR THR ILE ALA SEQRES 10 A 260 LYS GLU LEU ALA GLU LEU ASP PRO ASP ASN ARG ASP GLN SEQRES 11 A 260 TYR GLU ALA ASN LEU ALA ALA PHE LEU ALA GLU LEU GLU SEQRES 12 A 260 ARG LEU ASN GLN GLU LEU GLY GLN ILE LEU GLN PRO LEU SEQRES 13 A 260 PRO GLN ARG LYS PHE ILE VAL PHE HIS PRO SER TRP ALA SEQRES 14 A 260 TYR PHE ALA ARG ASP TYR ASN LEU VAL GLN ILE PRO ILE SEQRES 15 A 260 GLU VAL GLU GLY GLN GLU PRO SER ALA GLN GLU LEU LYS SEQRES 16 A 260 GLN LEU ILE ASP THR ALA LYS GLU ASN ASN LEU THR MET SEQRES 17 A 260 VAL PHE GLY GLU THR GLN PHE SER THR LYS SER SER GLU SEQRES 18 A 260 ALA ILE ALA ALA GLU ILE GLY ALA GLY VAL GLU LEU LEU SEQRES 19 A 260 ASP PRO LEU ALA ALA ASP TRP SER SER ASN LEU LYS ALA SEQRES 20 A 260 VAL ALA GLN LYS ILE ALA ASN ALA ASN SER ALA GLN PRO FORMUL 2 HOH *141(H2 O) HELIX 1 1 ILE A 55 GLY A 67 1 13 HELIX 2 2 LYS A 88 LEU A 95 1 8 HELIX 3 3 TRP A 112 ASN A 120 1 9 HELIX 4 4 SER A 183 ASP A 202 1 20 HELIX 5 5 ASN A 205 GLN A 232 1 28 HELIX 6 6 TRP A 246 TYR A 253 1 8 HELIX 7 7 GLN A 270 ASN A 283 1 14 HELIX 8 8 THR A 295 GLY A 306 1 12 HELIX 9 9 ASP A 318 SER A 335 1 18 SHEET 1 A 4 VAL A 70 VAL A 74 0 SHEET 2 A 4 MET A 49 VAL A 53 1 N VAL A 53 O SER A 73 SHEET 3 A 4 ALA A 100 LEU A 103 1 O VAL A 102 N THR A 52 SHEET 4 A 4 LYS A 124 ASP A 127 1 O LYS A 124 N TYR A 101 SHEET 1 B 4 VAL A 256 PRO A 259 0 SHEET 2 B 4 LYS A 238 VAL A 241 1 N PHE A 239 O ILE A 258 SHEET 3 B 4 MET A 286 GLU A 290 1 O PHE A 288 N ILE A 240 SHEET 4 B 4 GLY A 308 LEU A 312 1 O GLY A 308 N VAL A 287 CRYST1 62.578 76.503 127.151 90.00 90.00 90.00 C 2 2 21 8 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 0.015980 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013071 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007865 0.00000