HEADER HYDROLASE 21-MAY-14 4UMV TITLE CRYSTAL STRUCTURE OF A ZINC-TRANSPORTING PIB-TYPE ATPASE IN THE E2P TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC-TRANSPORTING ATPASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ZINC EFFLUX ATPASE; COMPND 5 EC: 3.6.3.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA SONNEI; SOURCE 3 ORGANISM_TAXID: 624; SOURCE 4 ATCC: 25931; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET52 KEYWDS CPC, CXXC, ATP-BINDING, HYDROLASE, ION TRANSPORT, METAL-BINDING, KEYWDS 2 NUCLEOTIDE-BINDING, TRANSMEMBRANE, TRANSPORT, HEAVY-METAL BINDING, KEYWDS 3 P-TYPE ATPASE, PIB-ATPASE, ZN2+ EXPORTING, ZINC TRANSPORT, PI- KEYWDS 4 ATPASE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.T.WANG,O.SITSEL,G.MELONI,H.E.AUTZEN,M.ANDERSSON,T.KLYMCHUK, AUTHOR 2 A.M.NIELSEN,D.C.REES,P.NISSEN,P.GOURDON REVDAT 5 10-JAN-24 4UMV 1 REMARK LINK REVDAT 4 29-OCT-14 4UMV 1 JRNL REVDAT 3 08-OCT-14 4UMV 1 REMARK REVDAT 2 27-AUG-14 4UMV 1 JRNL REVDAT 1 13-AUG-14 4UMV 0 JRNL AUTH K.WANG,O.SITSEL,G.MELONI,H.E.AUTZEN,M.ANDERSSON,T.KLYMCHUK, JRNL AUTH 2 A.M.NIELSEN,D.C.REES,P.NISSEN,P.GOURDON JRNL TITL STRUCTURE AND MECHANISM OF ZN(2+)-TRANSPORTING P-TYPE JRNL TITL 2 ATPASES. JRNL REF NATURE V. 514 518 2014 JRNL REFN ISSN 0028-0836 JRNL PMID 25132545 JRNL DOI 10.1038/NATURE13618 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 771 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 46.0870 - 5.8117 0.99 2514 131 0.2179 0.2695 REMARK 3 2 5.8117 - 4.6143 1.00 2459 129 0.2102 0.2696 REMARK 3 3 4.6143 - 4.0314 1.00 2436 129 0.1935 0.2683 REMARK 3 4 4.0314 - 3.6630 1.00 2417 127 0.2155 0.2905 REMARK 3 5 3.6630 - 3.4005 1.00 2414 127 0.2343 0.2913 REMARK 3 6 3.4005 - 3.2001 1.00 2437 128 0.2692 0.3385 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 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 : 0.007 4301 REMARK 3 ANGLE : 1.247 5865 REMARK 3 CHIRALITY : 0.083 747 REMARK 3 PLANARITY : 0.006 756 REMARK 3 DIHEDRAL : 18.254 1525 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 126:228) OR (RESSEQ 339:413) OR REMARK 3 (RESSEQ 664:730)) REMARK 3 ORIGIN FOR THE GROUP (A): 31.2865 -4.9532 289.1200 REMARK 3 T TENSOR REMARK 3 T11: 0.8679 T22: 0.5681 REMARK 3 T33: 0.5369 T12: -0.0128 REMARK 3 T13: 0.1905 T23: -0.0476 REMARK 3 L TENSOR REMARK 3 L11: 0.7189 L22: 0.5088 REMARK 3 L33: 1.2945 L12: 0.2562 REMARK 3 L13: -0.3329 L23: -0.8432 REMARK 3 S TENSOR REMARK 3 S11: -0.3022 S12: 0.3946 S13: -0.2906 REMARK 3 S21: -0.2087 S22: 0.1533 S23: -0.0562 REMARK 3 S31: 0.1375 S32: 0.0390 S33: 0.0954 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 229:338)) REMARK 3 ORIGIN FOR THE GROUP (A): 33.6929 -8.2189 341.3847 REMARK 3 T TENSOR REMARK 3 T11: 0.2844 T22: 0.2319 REMARK 3 T33: 0.6573 T12: 0.0289 REMARK 3 T13: 0.0146 T23: -0.0511 REMARK 3 L TENSOR REMARK 3 L11: 1.3666 L22: 1.7250 REMARK 3 L33: 2.8726 L12: 0.0564 REMARK 3 L13: 0.4843 L23: 0.5206 REMARK 3 S TENSOR REMARK 3 S11: 0.3461 S12: 0.2482 S13: -0.0450 REMARK 3 S21: 0.0075 S22: 0.2437 S23: -0.3241 REMARK 3 S31: 0.0827 S32: 0.3050 S33: -0.5112 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 444:559)) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0586 -10.3719 351.6151 REMARK 3 T TENSOR REMARK 3 T11: 0.1889 T22: 0.2540 REMARK 3 T33: 0.4397 T12: -0.0292 REMARK 3 T13: -0.0384 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 4.2771 L22: 5.1646 REMARK 3 L33: 4.5742 L12: -1.3010 REMARK 3 L13: -1.9316 L23: -0.4743 REMARK 3 S TENSOR REMARK 3 S11: 0.1450 S12: -0.5650 S13: 0.1452 REMARK 3 S21: 0.5051 S22: 0.0286 S23: -0.2200 REMARK 3 S31: -0.4196 S32: 0.0545 S33: -0.0996 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 414:443) OR (RESSEQ 560:663)) REMARK 3 ORIGIN FOR THE GROUP (A): 19.0438 -16.0916 321.1648 REMARK 3 T TENSOR REMARK 3 T11: 0.3154 T22: 0.2200 REMARK 3 T33: 0.3600 T12: 0.0578 REMARK 3 T13: 0.0847 T23: -0.0614 REMARK 3 L TENSOR REMARK 3 L11: 3.4016 L22: 2.6282 REMARK 3 L33: 3.9192 L12: -0.0936 REMARK 3 L13: -0.4959 L23: -0.9732 REMARK 3 S TENSOR REMARK 3 S11: 0.0100 S12: 0.1412 S13: -0.4080 REMARK 3 S21: -0.4307 S22: -0.0106 S23: -0.0641 REMARK 3 S31: 0.0086 S32: -0.1221 S33: -0.0433 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 4UMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060719. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15457 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.21000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.370 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: PDB ENTRY 3RFU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MGCL2, 200 MM LITHIUM ACETATE, REMARK 280 17 % V/V PEG2000-MME, 10 % V/V GLYCEROL AND 5 MM BME REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.48600 REMARK 290 SMTRY3 2 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 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 ASP A 5 REMARK 465 ASN A 6 REMARK 465 HIS A 7 REMARK 465 GLY A 8 REMARK 465 LYS A 9 REMARK 465 LYS A 10 REMARK 465 ALA A 11 REMARK 465 PRO A 12 REMARK 465 GLN A 13 REMARK 465 PHE A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 PHE A 17 REMARK 465 LYS A 18 REMARK 465 PRO A 19 REMARK 465 LEU A 20 REMARK 465 THR A 21 REMARK 465 THR A 22 REMARK 465 VAL A 23 REMARK 465 GLN A 24 REMARK 465 ASN A 25 REMARK 465 ALA A 26 REMARK 465 ASN A 27 REMARK 465 ASP A 28 REMARK 465 CYS A 29 REMARK 465 CYS A 30 REMARK 465 CYS A 31 REMARK 465 ASP A 32 REMARK 465 GLY A 33 REMARK 465 ALA A 34 REMARK 465 CYS A 35 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 SER A 38 REMARK 465 PRO A 39 REMARK 465 THR A 40 REMARK 465 LEU A 41 REMARK 465 SER A 42 REMARK 465 GLU A 43 REMARK 465 ASN A 44 REMARK 465 VAL A 45 REMARK 465 SER A 46 REMARK 465 GLY A 47 REMARK 465 THR A 48 REMARK 465 ARG A 49 REMARK 465 TYR A 50 REMARK 465 SER A 51 REMARK 465 TRP A 52 REMARK 465 LYS A 53 REMARK 465 VAL A 54 REMARK 465 SER A 55 REMARK 465 GLY A 56 REMARK 465 MET A 57 REMARK 465 ASP A 58 REMARK 465 CYS A 59 REMARK 465 ALA A 60 REMARK 465 ALA A 61 REMARK 465 CYS A 62 REMARK 465 ALA A 63 REMARK 465 ARG A 64 REMARK 465 LYS A 65 REMARK 465 VAL A 66 REMARK 465 GLU A 67 REMARK 465 ASN A 68 REMARK 465 ALA A 69 REMARK 465 VAL A 70 REMARK 465 ARG A 71 REMARK 465 GLN A 72 REMARK 465 LEU A 73 REMARK 465 ALA A 74 REMARK 465 GLY A 75 REMARK 465 VAL A 76 REMARK 465 ASN A 77 REMARK 465 GLN A 78 REMARK 465 VAL A 79 REMARK 465 GLN A 80 REMARK 465 VAL A 81 REMARK 465 LEU A 82 REMARK 465 PHE A 83 REMARK 465 ALA A 84 REMARK 465 THR A 85 REMARK 465 GLU A 86 REMARK 465 LYS A 87 REMARK 465 LEU A 88 REMARK 465 VAL A 89 REMARK 465 VAL A 90 REMARK 465 ASP A 91 REMARK 465 ALA A 92 REMARK 465 ASP A 93 REMARK 465 ASN A 94 REMARK 465 ASP A 95 REMARK 465 ILE A 96 REMARK 465 ARG A 97 REMARK 465 ALA A 98 REMARK 465 GLN A 99 REMARK 465 VAL A 100 REMARK 465 GLU A 101 REMARK 465 SER A 102 REMARK 465 ALA A 103 REMARK 465 VAL A 104 REMARK 465 GLN A 105 REMARK 465 LYS A 106 REMARK 465 ALA A 107 REMARK 465 GLY A 108 REMARK 465 TYR A 109 REMARK 465 SER A 110 REMARK 465 LEU A 111 REMARK 465 ARG A 112 REMARK 465 ASP A 113 REMARK 465 GLU A 114 REMARK 465 GLN A 115 REMARK 465 ALA A 116 REMARK 465 ALA A 117 REMARK 465 ASP A 118 REMARK 465 GLU A 119 REMARK 465 PRO A 120 REMARK 465 GLN A 121 REMARK 465 ALA A 122 REMARK 465 SER A 123 REMARK 465 ARG A 124 REMARK 465 LEU A 125 REMARK 465 ARG A 731 REMARK 465 ARG A 732 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 132 CG1 CG2 CD1 REMARK 470 VAL A 711 CG1 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 382 CG CD1 CD2 CE1 CE2 CZ OH 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 ILE A 183 N THR A 185 1.56 REMARK 500 CD2 LEU A 129 CB ILE A 132 1.84 REMARK 500 O ASP A 714 N ALA A 717 1.89 REMARK 500 O PRO A 369 O LEU A 372 1.92 REMARK 500 O ILE A 183 N LEU A 186 1.99 REMARK 500 O ASP A 714 N GLY A 716 1.99 REMARK 500 O SER A 376 N GLN A 378 2.04 REMARK 500 CA LYS A 693 CE2 PHE A 696 2.05 REMARK 500 O ALA A 395 N VAL A 397 2.06 REMARK 500 CB LEU A 709 CB ALA A 713 2.07 REMARK 500 CA LEU A 709 CB ALA A 713 2.11 REMARK 500 O LEU A 692 CD2 PHE A 696 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 NH2 ARG A 241 O GLU A 489 1455 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU A 709 CA LEU A 709 C 0.173 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 372 N - CA - C ANGL. DEV. = -17.1 DEGREES REMARK 500 LEU A 692 CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 LEU A 709 CA - C - O ANGL. DEV. = 14.5 DEGREES REMARK 500 LEU A 709 CA - C - N ANGL. DEV. = -14.7 DEGREES REMARK 500 ALA A 710 N - CA - CB ANGL. DEV. = 11.3 DEGREES 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 GLU A 127 -26.67 -146.58 REMARK 500 ASN A 148 34.53 75.38 REMARK 500 HIS A 149 -61.20 -28.84 REMARK 500 SER A 177 40.90 -96.35 REMARK 500 ILE A 183 -97.39 83.94 REMARK 500 GLU A 184 -26.41 -21.23 REMARK 500 LEU A 195 -22.35 -33.02 REMARK 500 PHE A 196 -14.44 -145.60 REMARK 500 ALA A 233 46.60 -93.65 REMARK 500 LEU A 234 114.94 1.93 REMARK 500 GLU A 237 -179.27 58.11 REMARK 500 THR A 238 143.06 84.31 REMARK 500 ARG A 243 -117.30 -96.27 REMARK 500 ASN A 244 48.89 -67.81 REMARK 500 PRO A 278 -75.82 -42.09 REMARK 500 GLU A 284 40.67 -106.62 REMARK 500 PRO A 293 144.77 -37.76 REMARK 500 ALA A 306 138.39 72.15 REMARK 500 ARG A 311 136.64 74.92 REMARK 500 PRO A 321 -73.78 -43.12 REMARK 500 GLU A 338 46.66 -71.24 REMARK 500 ARG A 339 -9.65 -166.62 REMARK 500 ALA A 357 -72.49 -55.41 REMARK 500 PHE A 373 -29.88 78.95 REMARK 500 ALA A 374 83.41 52.75 REMARK 500 SER A 376 94.32 -53.01 REMARK 500 TRP A 377 -27.24 -25.65 REMARK 500 ALA A 395 -164.91 -63.51 REMARK 500 LEU A 396 -55.66 47.06 REMARK 500 ARG A 414 44.47 -87.76 REMARK 500 LYS A 419 -117.28 -68.62 REMARK 500 ARG A 429 -16.20 -143.45 REMARK 500 LYS A 437 -70.41 -93.09 REMARK 500 THR A 438 100.86 -52.11 REMARK 500 THR A 442 -157.62 -113.39 REMARK 500 PRO A 493 -168.34 -115.00 REMARK 500 THR A 494 -103.67 49.64 REMARK 500 ALA A 495 128.76 56.84 REMARK 500 GLU A 496 -68.91 -137.61 REMARK 500 SER A 497 -74.12 -86.83 REMARK 500 GLN A 498 95.38 66.57 REMARK 500 ALA A 500 7.68 -67.53 REMARK 500 VAL A 502 -42.95 90.80 REMARK 500 SER A 504 -9.27 67.01 REMARK 500 ALA A 519 -152.34 -75.96 REMARK 500 ALA A 520 -91.04 -64.14 REMARK 500 ASN A 548 -103.21 53.46 REMARK 500 ASP A 549 40.59 -144.70 REMARK 500 ALA A 639 94.50 -164.41 REMARK 500 ALA A 640 -60.99 51.05 REMARK 500 REMARK 500 THIS ENTRY HAS 61 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF A1732 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 436 OD2 REMARK 620 2 BEF A1732 F1 91.7 REMARK 620 3 BEF A1732 F2 120.0 110.5 REMARK 620 4 BEF A1732 F3 111.0 107.7 113.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1731 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 438 O REMARK 620 2 ASP A 628 OD2 77.3 REMARK 620 3 ASP A 628 OD1 90.6 87.1 REMARK 620 4 BEF A1732 BE 97.1 174.3 94.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1731 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF A 1732 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UMW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A ZINC-TRANSPORTING PIB-TYPE ATPASE IN E2.PI REMARK 900 STATE DBREF 4UMV A 1 732 UNP Q3YW59 Q3YW59_SHISS 1 732 SEQRES 1 A 732 MET SER THR PRO ASP ASN HIS GLY LYS LYS ALA PRO GLN SEQRES 2 A 732 PHE ALA ALA PHE LYS PRO LEU THR THR VAL GLN ASN ALA SEQRES 3 A 732 ASN ASP CYS CYS CYS ASP GLY ALA CYS SER SER SER PRO SEQRES 4 A 732 THR LEU SER GLU ASN VAL SER GLY THR ARG TYR SER TRP SEQRES 5 A 732 LYS VAL SER GLY MET ASP CYS ALA ALA CYS ALA ARG LYS SEQRES 6 A 732 VAL GLU ASN ALA VAL ARG GLN LEU ALA GLY VAL ASN GLN SEQRES 7 A 732 VAL GLN VAL LEU PHE ALA THR GLU LYS LEU VAL VAL ASP SEQRES 8 A 732 ALA ASP ASN ASP ILE ARG ALA GLN VAL GLU SER ALA VAL SEQRES 9 A 732 GLN LYS ALA GLY TYR SER LEU ARG ASP GLU GLN ALA ALA SEQRES 10 A 732 ASP GLU PRO GLN ALA SER ARG LEU LYS GLU ASN LEU PRO SEQRES 11 A 732 LEU ILE THR LEU ILE VAL MET MET ALA ILE SER TRP GLY SEQRES 12 A 732 LEU GLU GLN PHE ASN HIS PRO PHE GLY GLN LEU ALA PHE SEQRES 13 A 732 ILE ALA THR THR LEU VAL GLY LEU TYR PRO ILE ALA ARG SEQRES 14 A 732 GLN ALA LEU ARG LEU ILE LYS SER GLY SER TYR PHE ALA SEQRES 15 A 732 ILE GLU THR LEU MET SER VAL ALA ALA ILE GLY ALA LEU SEQRES 16 A 732 PHE ILE GLY ALA THR ALA GLU ALA ALA MET VAL LEU LEU SEQRES 17 A 732 LEU PHE LEU ILE GLY GLU ARG LEU GLU GLY TRP ALA ALA SEQRES 18 A 732 SER ARG ALA ARG GLN GLY VAL SER ALA LEU MET ALA LEU SEQRES 19 A 732 LYS PRO GLU THR ALA THR ARG LEU ARG ASN GLY GLU ARG SEQRES 20 A 732 GLU GLU VAL ALA ILE ASN SER LEU ARG PRO GLY ASP VAL SEQRES 21 A 732 ILE GLU VAL ALA ALA GLY GLY ARG LEU PRO ALA ASP GLY SEQRES 22 A 732 LYS LEU LEU SER PRO PHE ALA SER PHE ASP GLU SER ALA SEQRES 23 A 732 LEU THR GLY GLU SER ILE PRO VAL GLU ARG ALA THR GLY SEQRES 24 A 732 ASP LYS VAL PRO ALA GLY ALA THR SER VAL ASP ARG LEU SEQRES 25 A 732 VAL THR LEU GLU VAL LEU SER GLU PRO GLY ALA SER ALA SEQRES 26 A 732 ILE ASP ARG ILE LEU LYS LEU ILE GLU GLU ALA GLU GLU SEQRES 27 A 732 ARG ARG ALA PRO ILE GLU ARG PHE ILE ASP ARG PHE SER SEQRES 28 A 732 ARG ILE TYR THR PRO ALA ILE MET ALA VAL ALA LEU LEU SEQRES 29 A 732 VAL THR LEU VAL PRO PRO LEU LEU PHE ALA ALA SER TRP SEQRES 30 A 732 GLN GLU TRP ILE TYR LYS GLY LEU THR LEU LEU LEU ILE SEQRES 31 A 732 GLY CYS PRO CYS ALA LEU VAL ILE SER THR PRO ALA ALA SEQRES 32 A 732 ILE THR SER GLY LEU ALA ALA ALA ALA ARG ARG GLY ALA SEQRES 33 A 732 LEU ILE LYS GLY GLY ALA ALA LEU GLU GLN LEU GLY ARG SEQRES 34 A 732 VAL THR GLN VAL ALA PHE ASP LYS THR GLY THR LEU THR SEQRES 35 A 732 VAL GLY LYS PRO ARG VAL THR ALA ILE HIS PRO ALA THR SEQRES 36 A 732 GLY ILE SER GLU SER GLU LEU LEU THR LEU ALA ALA ALA SEQRES 37 A 732 VAL GLU GLN GLY ALA THR HIS PRO LEU ALA GLN ALA ILE SEQRES 38 A 732 VAL ARG GLU ALA GLN VAL ALA GLU LEU ALA ILE PRO THR SEQRES 39 A 732 ALA GLU SER GLN ARG ALA LEU VAL GLY SER GLY ILE GLU SEQRES 40 A 732 ALA GLN VAL ASN GLY GLU ARG VAL LEU ILE CYS ALA ALA SEQRES 41 A 732 GLY LYS HIS PRO ALA ASP ALA PHE ALA GLY LEU ILE ASN SEQRES 42 A 732 GLU LEU GLU SER ALA GLY GLN THR VAL VAL LEU VAL VAL SEQRES 43 A 732 ARG ASN ASP ASP VAL LEU GLY ILE ILE ALA LEU GLN ASP SEQRES 44 A 732 THR LEU ARG ALA ASP ALA ALA THR ALA ILE SER GLU LEU SEQRES 45 A 732 ASN ALA LEU GLY VAL LYS GLY VAL ILE LEU THR GLY ASP SEQRES 46 A 732 ASN PRO ARG ALA ALA ALA ALA ILE ALA GLY GLU LEU GLY SEQRES 47 A 732 LEU GLU PHE LYS ALA GLY LEU LEU PRO GLU ASP LYS VAL SEQRES 48 A 732 LYS ALA VAL THR LYS LEU ASN GLN HIS ALA PRO LEU ALA SEQRES 49 A 732 MET VAL GLY ASP GLY ILE ASN ASP ALA PRO ALA MET LYS SEQRES 50 A 732 ALA ALA ALA ILE GLY ILE ALA MET GLY SER GLY THR ASP SEQRES 51 A 732 VAL ALA LEU GLU THR ALA ASP ALA ALA LEU THR HIS ASN SEQRES 52 A 732 HIS LEU ARG GLY LEU VAL GLN MET ILE GLU LEU ALA ARG SEQRES 53 A 732 ALA THR HIS ALA ASN ILE ARG GLN ASN ILE THR ILE ALA SEQRES 54 A 732 LEU GLY LEU LYS GLY ILE PHE LEU VAL THR THR LEU LEU SEQRES 55 A 732 GLY MET THR GLY LEU TRP LEU ALA VAL LEU ALA ASP THR SEQRES 56 A 732 GLY ALA THR VAL LEU VAL THR ALA ASN ALA LEU ARG LEU SEQRES 57 A 732 LEU ARG ARG ARG HET MG A1731 1 HET BEF A1732 4 HETNAM MG MAGNESIUM ION HETNAM BEF BERYLLIUM TRIFLUORIDE ION FORMUL 2 MG MG 2+ FORMUL 3 BEF BE F3 1- HELIX 1 1 LEU A 129 LEU A 144 1 16 HELIX 2 2 ASN A 148 SER A 177 1 30 HELIX 3 3 GLU A 184 GLY A 198 1 15 HELIX 4 4 ALA A 199 MET A 232 1 34 HELIX 5 5 ALA A 251 LEU A 255 5 5 HELIX 6 6 GLU A 284 GLY A 289 1 6 HELIX 7 7 GLU A 320 ALA A 323 5 4 HELIX 8 8 SER A 324 GLU A 338 1 15 HELIX 9 9 ARG A 345 LEU A 372 1 28 HELIX 10 10 SER A 376 GLY A 391 1 16 HELIX 11 11 PRO A 393 ILE A 398 1 6 HELIX 12 12 ILE A 398 ARG A 414 1 17 HELIX 13 13 GLY A 420 GLY A 428 1 9 HELIX 14 14 SER A 458 GLN A 471 1 14 HELIX 15 15 HIS A 475 ALA A 488 1 14 HELIX 16 16 ALA A 525 ALA A 527 5 3 HELIX 17 17 PHE A 528 ALA A 538 1 11 HELIX 18 18 ASP A 564 LEU A 575 1 12 HELIX 19 19 ASN A 586 LEU A 597 1 12 HELIX 20 20 LEU A 606 GLN A 619 1 14 HELIX 21 21 GLY A 629 ASN A 631 5 3 HELIX 22 22 ASP A 632 LYS A 637 1 6 HELIX 23 23 THR A 649 ALA A 656 1 8 HELIX 24 24 LEU A 665 LEU A 702 1 38 HELIX 25 25 THR A 715 ALA A 725 1 11 SHEET 1 AA 2 ARG A 241 LEU A 242 0 SHEET 2 AA 2 ARG A 247 GLU A 248 -1 O GLU A 248 N ARG A 241 SHEET 1 AB 4 VAL A 260 VAL A 263 0 SHEET 2 AB 4 VAL A 313 VAL A 317 -1 O VAL A 313 N VAL A 263 SHEET 3 AB 4 GLY A 273 LEU A 275 -1 O LYS A 274 N GLU A 316 SHEET 4 AB 4 LYS A 301 VAL A 302 -1 O VAL A 302 N GLY A 273 SHEET 1 AC 2 PHE A 279 PHE A 282 0 SHEET 2 AC 2 VAL A 294 ALA A 297 -1 O VAL A 294 N PHE A 282 SHEET 1 AD 7 ALA A 416 ILE A 418 0 SHEET 2 AD 7 ALA A 658 LEU A 660 -1 O ALA A 659 N LEU A 417 SHEET 3 AD 7 ILE A 641 MET A 645 1 O ALA A 644 N LEU A 660 SHEET 4 AD 7 LEU A 623 GLY A 627 1 O LEU A 623 N ILE A 641 SHEET 5 AD 7 GLN A 432 PHE A 435 1 O GLN A 432 N ALA A 624 SHEET 6 AD 7 LYS A 578 LEU A 582 1 O LYS A 578 N VAL A 433 SHEET 7 AD 7 GLU A 600 LYS A 602 1 O GLU A 600 N ILE A 581 SHEET 1 AE 5 THR A 442 PRO A 453 0 SHEET 2 AE 5 ASP A 550 LEU A 561 -1 O ILE A 554 N HIS A 452 SHEET 3 AE 5 THR A 541 ARG A 547 -1 O THR A 541 N LEU A 557 SHEET 4 AE 5 GLU A 513 CYS A 518 -1 O LEU A 516 N VAL A 546 SHEET 5 AE 5 ILE A 506 VAL A 510 -1 O ILE A 506 N ILE A 517 LINK OD2 ASP A 436 BE BEF A1732 1555 1555 1.90 LINK O THR A 438 MG MG A1731 1555 1555 2.45 LINK OD2 ASP A 628 MG MG A1731 1555 1555 1.29 LINK OD1 ASP A 628 MG MG A1731 1555 1555 1.88 LINK MG MG A1731 BE BEF A1732 1555 1555 2.85 CISPEP 1 LYS A 126 GLU A 127 0 -17.07 CISPEP 2 ALA A 306 THR A 307 0 -15.56 CISPEP 3 MET A 704 THR A 705 0 -1.04 CISPEP 4 THR A 705 GLY A 706 0 0.19 SITE 1 AC1 5 ASP A 436 THR A 438 ASP A 628 GLY A 629 SITE 2 AC1 5 BEF A1732 SITE 1 AC2 8 SER A 285 GLY A 289 ASP A 436 THR A 438 SITE 2 AC2 8 THR A 583 ASP A 628 ASN A 631 MG A1731 CRYST1 54.462 60.972 141.523 90.00 95.99 90.00 P 1 21 1 2 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 0.018361 0.000000 0.001927 0.00000 SCALE2 0.000000 0.016401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007105 0.00000