HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 05-JUL-04 1TXL TITLE CRYSTAL STRUCTURE OF METAL-BINDING PROTEIN YODA FROM E. COLI, PFAM TITLE 2 DUF149 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METAL-BINDING PROTEIN YODA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CADMIUM-INDUCED PROTEIN YODA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YODA, B1973; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS YODA, E.COLI, STRUCTURAL GENOMICS, NEW FOLD, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 NYSGXRC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.ESWARAMOORTHY,S.SWAMINATHAN,S.K.BURLEY,NEW YORK SGX RESEARCH CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 5 03-FEB-21 1TXL 1 AUTHOR REMARK LINK REVDAT 4 24-FEB-09 1TXL 1 VERSN REVDAT 3 25-JAN-05 1TXL 1 AUTHOR KEYWDS REMARK REVDAT 2 27-JUL-04 1TXL 1 REMARK REVDAT 1 20-JUL-04 1TXL 0 JRNL AUTH S.ESWARAMOORTHY,S.SWAMINATHAN JRNL TITL CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YODA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 20185 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) : 0.228 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 973 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 : 1537 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 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) : 1.245 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) : 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A ZN ATOM COORDINATING TO HIS166, REMARK 3 HIS175 AND HIS177 HAS BEEN LOCATED IN THE PUTATIVE ACTIVE-SITE REMARK 3 CAVITY. FOLLOWED BY ZN, CONTINUOUS ELECTRON DENSITY HAS BEEN REMARK 3 OBSERVED. THIS DENSITY COULD ACCOMODATE A BRANCHED CARBOHYDRATE REMARK 3 CHAIN AND A PO4 HEAD GROUP. A PROBABLE SUBSTRATE SUSPECTED TO BE REMARK 3 PRESENT IN THE STRUCTURE HAS NOT BEEN ADDED TO THE MODEL BECAUSE REMARK 3 IT IS NOT KNOWN FOR SURE. WATER MOLECULES LOCATED AROUND THE ZN REMARK 3 ATOM IN THE ACTIVE SITE CAVITY HAVE TO BE TREATED WITH CARE. REMARK 3 WATER MOLECULE 218 MAY BE REPLACED WITH A PO4. REMARK 4 REMARK 4 1TXL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-03; 25-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X12B; X12C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979; 1.2804, 1.2818, 1.2200 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CBASS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 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 (%) : 96.3 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.13700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, PH 7.2, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 32.62000 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 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 ALA A 1 REMARK 465 ILE A 2 REMARK 465 ARG A 3 REMARK 465 LEU A 4 REMARK 465 TYR A 5 REMARK 465 LYS A 6 REMARK 465 LEU A 7 REMARK 465 ALA A 8 REMARK 465 VAL A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 GLY A 12 REMARK 465 VAL A 13 REMARK 465 PHE A 14 REMARK 465 ILE A 15 REMARK 465 VAL A 16 REMARK 465 SER A 17 REMARK 465 ALA A 18 REMARK 465 PRO A 19 REMARK 465 ALA A 20 REMARK 465 PHE A 21 REMARK 465 SER A 22 REMARK 465 HIS A 23 REMARK 465 GLY A 24 REMARK 465 HIS A 25 REMARK 465 HIS A 26 REMARK 465 SER A 27 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 ASP A 111 53.86 37.93 REMARK 500 ASN A 119 -132.54 61.19 REMARK 500 ASP A 165 26.85 -143.06 REMARK 500 PRO A 170 126.79 -38.68 REMARK 500 ARG A 171 141.17 177.29 REMARK 500 ASP A 183 -62.69 -92.31 REMARK 500 TRP A 195 80.74 -158.22 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 ZN A 216 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 166 NE2 REMARK 620 2 HIS A 175 NE2 105.3 REMARK 620 3 HIS A 177 NE2 101.8 104.1 REMARK 620 4 HOH A 218 O 100.8 122.3 119.6 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 ZN A 216 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T1465 RELATED DB: TARGETDB DBREF 1TXL A 1 215 UNP P76344 YODA_ECOLI 2 216 SEQRES 1 A 215 ALA ILE ARG LEU TYR LYS LEU ALA VAL ALA LEU GLY VAL SEQRES 2 A 215 PHE ILE VAL SER ALA PRO ALA PHE SER HIS GLY HIS HIS SEQRES 3 A 215 SER HIS GLY LYS PRO LEU THR GLU VAL GLU GLN LYS ALA SEQRES 4 A 215 ALA ASN GLY VAL PHE ASP ASP ALA ASN VAL GLN ASN ARG SEQRES 5 A 215 THR LEU SER ASP TRP ASP GLY VAL TRP GLN SER VAL TYR SEQRES 6 A 215 PRO LEU LEU GLN SER GLY LYS LEU ASP PRO VAL PHE GLN SEQRES 7 A 215 LYS LYS ALA ASP ALA ASP LYS THR LYS THR PHE ALA GLU SEQRES 8 A 215 ILE LYS ASP TYR TYR HIS LYS GLY TYR ALA THR ASP ILE SEQRES 9 A 215 GLU MET ILE GLY ILE GLU ASP GLY ILE VAL GLU PHE HIS SEQRES 10 A 215 ARG ASN ASN GLU THR THR SER CYS LYS TYR ASP TYR ASP SEQRES 11 A 215 GLY TYR LYS ILE LEU THR TYR LYS SER GLY LYS LYS GLY SEQRES 12 A 215 VAL ARG TYR LEU PHE GLU CYS LYS ASP PRO GLU SER LYS SEQRES 13 A 215 ALA PRO LYS TYR ILE GLN PHE SER ASP HIS ILE ILE ALA SEQRES 14 A 215 PRO ARG LYS SER SER HIS PHE HIS ILE PHE MET GLY ASN SEQRES 15 A 215 ASP SER GLN GLN SER LEU LEU ASN GLU MET GLU ASN TRP SEQRES 16 A 215 PRO THR TYR TYR PRO TYR GLN LEU SER SER GLU GLU VAL SEQRES 17 A 215 VAL GLU GLU MET MET SER HIS HET ZN A 216 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *224(H2 O) HELIX 1 1 THR A 33 ASN A 41 1 9 HELIX 2 2 ASP A 45 VAL A 49 5 5 HELIX 3 3 THR A 53 ASP A 58 5 6 HELIX 4 4 VAL A 64 SER A 70 1 7 HELIX 5 5 LEU A 73 ASP A 84 1 12 HELIX 6 6 THR A 88 ALA A 101 1 14 HELIX 7 7 SER A 184 ASN A 190 1 7 HELIX 8 8 SER A 204 HIS A 215 1 12 SHEET 1 A 9 GLU A 121 CYS A 125 0 SHEET 2 A 9 ILE A 113 ARG A 118 -1 N PHE A 116 O THR A 123 SHEET 3 A 9 ILE A 104 GLU A 110 -1 N GLY A 108 O GLU A 115 SHEET 4 A 9 GLY A 59 SER A 63 -1 N TRP A 61 O ILE A 107 SHEET 5 A 9 THR A 197 PRO A 200 -1 O TYR A 199 N GLN A 62 SHEET 6 A 9 PHE A 176 GLY A 181 -1 N PHE A 176 O TYR A 198 SHEET 7 A 9 TYR A 160 SER A 164 -1 N SER A 164 O HIS A 177 SHEET 8 A 9 LYS A 142 GLU A 149 -1 N TYR A 146 O PHE A 163 SHEET 9 A 9 ASP A 128 THR A 136 -1 N LEU A 135 O GLY A 143 SSBOND 1 CYS A 125 CYS A 150 1555 1555 2.04 LINK NE2 HIS A 166 ZN ZN A 216 1555 1555 2.16 LINK NE2 HIS A 175 ZN ZN A 216 1555 1555 2.41 LINK NE2 HIS A 177 ZN ZN A 216 1555 1555 1.93 LINK ZN ZN A 216 O HOH A 218 1555 1555 2.28 SITE 1 AC1 4 HIS A 166 HIS A 175 HIS A 177 HOH A 218 CRYST1 40.240 65.240 41.340 90.00 117.66 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 0.024851 0.000000 0.013025 0.00000 SCALE2 0.000000 0.015328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027311 0.00000