HEADER STRESS PROTEIN/LIPOCALIN 27-MAR-03 1OEJ TITLE YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH NO ADDED IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YODA; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS STRESS PROTEIN/LIPOCALIN, STRESS PROTEIN, LIPOCALIN, YODA EXPDTA X-RAY DIFFRACTION AUTHOR G.DAVID,K.BLONDEAU,M.RENOUARD,S.PENEL,A.LEWIT-BENTLEY REVDAT 3 24-FEB-09 1OEJ 1 VERSN REVDAT 2 30-OCT-03 1OEJ 1 JRNL REVDAT 1 15-AUG-03 1OEJ 0 JRNL AUTH G.DAVID,K.BLONDEAU,M.SCHILTZ,S.PENEL, JRNL AUTH 2 A.LEWIT-BENTLEY JRNL TITL YODA FROM ESCHERICHIA COLI IS A METAL-BINDING, JRNL TITL 2 LIPOCALIN-LIKE PROTEIN JRNL REF J.BIOL.CHEM. V. 278 43728 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12909634 JRNL DOI 10.1074/JBC.M304484200 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 74.27 REMARK 3 NUMBER OF REFLECTIONS : 12128 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 + TEST SET) : 0.18371 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.25226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 653 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 : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.107 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.508 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45 REMARK 3 B22 (A**2) : 0.83 REMARK 3 B33 (A**2) : -0.87 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : -0.52 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.199 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.189 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.702 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. THE FIRST 6 RESIDUES AT THE N-TERMINUS ARE REMARK 3 DISORDERED REMARK 4 REMARK 4 1OEJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-03. REMARK 100 THE PDBE ID CODE IS EBI-12470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6027 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 14.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.5 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.58800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE, CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 1OEE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN, REMARK 280 30% PEG 10000, 100 MM SODIUM CACODYLATE, PH = 6.5 REMARK 280 200 MM SODIUM ACETATE 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 32.27900 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 GENERATING THE BIOMOLECULE 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: PQS 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 HIS A 1 REMARK 465 GLY A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 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 ASP A 34 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 161 CB - CG - OD2 ANGL. DEV. = 6.2 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 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 97 92.65 -39.92 REMARK 500 ASN A 98 -12.17 73.11 REMARK 500 ASP A 143 30.96 -150.85 REMARK 500 HIS A 144 19.89 59.69 REMARK 500 ARG A 149 135.47 179.56 REMARK 500 ASP A 161 -64.93 -91.12 REMARK 500 SER A 192 -103.77 -110.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLU A 171 23.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): 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 NI A1194 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 144 NE2 REMARK 620 2 HIS A 153 NE2 99.9 REMARK 620 3 HIS A 155 NE2 102.2 109.8 REMARK 620 4 HOH A2091 O 127.1 118.8 97.1 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 NI A1194 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OEE RELATED DB: PDB REMARK 900 YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH REMARK 900 CADMIUM IONS REMARK 900 RELATED ID: 1OEK RELATED DB: PDB REMARK 900 YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH REMARK 900 ZINC IONS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE: MAIRLYKLAVALGVFIVSAPAFS REMARK 999 THAT IS INCLUDED THE SWISPROT RECORD REMARK 999 UPSTREAM OF THE SEQUENCE CRYSTALLISED, REMARK 999 CORRESPONDS TO A SIGNAL SEQUENCE THAT REMARK 999 IS CLEAVED IN THE MATURE PROTEIN. DBREF 1OEJ A 1 193 UNP P76344 YODA_ECOLI 24 216 SEQRES 1 A 193 HIS GLY HIS HIS SER HIS GLY LYS PRO LEU THR GLU VAL SEQRES 2 A 193 GLU GLN LYS ALA ALA ASN GLY VAL PHE ASP ASP ALA ASN SEQRES 3 A 193 VAL GLN ASN ARG THR LEU SER ASP TRP ASP GLY VAL TRP SEQRES 4 A 193 GLN SER VAL TYR PRO LEU LEU GLN SER GLY LYS LEU ASP SEQRES 5 A 193 PRO VAL PHE GLN LYS LYS ALA ASP ALA ASP LYS THR LYS SEQRES 6 A 193 THR PHE ALA GLU ILE LYS ASP TYR TYR HIS LYS GLY TYR SEQRES 7 A 193 ALA THR ASP ILE GLU MET ILE GLY ILE GLU ASP GLY ILE SEQRES 8 A 193 VAL GLU PHE HIS ARG ASN ASN GLU THR THR SER CYS LYS SEQRES 9 A 193 TYR ASP TYR ASP GLY TYR LYS ILE LEU THR TYR LYS SER SEQRES 10 A 193 GLY LYS LYS GLY VAL ARG TYR LEU PHE GLU CYS LYS ASP SEQRES 11 A 193 PRO GLU SER LYS ALA PRO LYS TYR ILE GLN PHE SER ASP SEQRES 12 A 193 HIS ILE ILE ALA PRO ARG LYS SER SER HIS PHE HIS ILE SEQRES 13 A 193 PHE MET GLY ASN ASP SER GLN GLN SER LEU LEU ASN GLU SEQRES 14 A 193 MET GLU ASN TRP PRO THR TYR TYR PRO TYR GLN LEU SER SEQRES 15 A 193 SER GLU GLU VAL VAL GLU GLU MET MET SER HIS HET NI A1194 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *101(H2 O1) HELIX 1 1 THR A 11 ASN A 19 1 9 HELIX 2 2 ASP A 23 VAL A 27 5 5 HELIX 3 3 THR A 31 ASP A 36 5 6 HELIX 4 4 VAL A 42 SER A 48 1 7 HELIX 5 5 LEU A 51 ASP A 62 1 12 HELIX 6 6 THR A 66 ALA A 79 1 14 HELIX 7 7 SER A 162 GLU A 169 1 8 HELIX 8 8 SER A 182 SER A 192 1 11 SHEET 1 AA 9 GLU A 99 LYS A 104 0 SHEET 2 AA 9 ILE A 91 ARG A 96 -1 O VAL A 92 N CYS A 103 SHEET 3 AA 9 MET A 84 GLU A 88 -1 O MET A 84 N HIS A 95 SHEET 4 AA 9 GLY A 37 SER A 41 -1 O GLY A 37 N ILE A 87 SHEET 5 AA 9 THR A 175 PRO A 178 -1 O TYR A 177 N GLN A 40 SHEET 6 AA 9 PHE A 154 GLY A 159 -1 O PHE A 154 N TYR A 176 SHEET 7 AA 9 TYR A 138 SER A 142 -1 O TYR A 138 N GLY A 159 SHEET 8 AA 9 LYS A 120 GLU A 127 -1 O TYR A 124 N PHE A 141 SHEET 9 AA 9 ASP A 106 THR A 114 -1 O ASP A 106 N GLU A 127 SSBOND 1 CYS A 103 CYS A 128 1555 1555 2.00 LINK NI NI A1194 NE2 HIS A 144 1555 1555 2.26 LINK NI NI A1194 NE2 HIS A 153 1555 1555 2.26 LINK NI NI A1194 NE2 HIS A 155 1555 1555 2.16 LINK NI NI A1194 O HOH A2091 1555 1555 2.50 SITE 1 AC1 4 HIS A 144 HIS A 153 HIS A 155 HOH A2091 CRYST1 40.348 64.558 41.499 90.00 117.83 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 0.024784 0.000000 0.013084 0.00000 SCALE2 0.000000 0.015490 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027249 0.00000 MASTER 300 0 1 8 9 0 1 6 0 0 0 15 END