HEADER STRUCTURAL GENOMICS 07-JUL-99 1QU9 TITLE 1.2 A CRYSTAL STRUCTURE OF YJGF GENE PRODUCT FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: YJGF PROTEIN; COMPND 3 CHAIN: A, B, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR K.VOLZ REVDAT 3 31-JAN-18 1QU9 1 REMARK REVDAT 2 24-FEB-09 1QU9 1 VERSN REVDAT 1 01-DEC-99 1QU9 0 JRNL AUTH K.VOLZ JRNL TITL A TEST CASE FOR STRUCTURE-BASED FUNCTIONAL ASSIGNMENT: THE JRNL TITL 2 1.2 A CRYSTAL STRUCTURE OF THE YJGF GENE PRODUCT FROM JRNL TITL 3 ESCHERICHIA COLI JRNL REF PROTEIN SCI. V. 8 2428 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10595546 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 103863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 112350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2841 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 474 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.61 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.031 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.048 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.018 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.131 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.164 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.142 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : 0.132 ; 0.500 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) : 3.600 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 11.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 15.600; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.727 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.124 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.145 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.794 ; 1.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 75 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.961 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SMART, SAINT REMARK 200 DATA SCALING SOFTWARE : SMART, SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 112350 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS HCL, 2.35 M AMMONIUM REMARK 280 SULPHATE, PH 8.1, MICRODIALYSIS, TEMPERATURE 4K, TEMPERATURE REMARK 280 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-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 0.00000 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 0.00000 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 256 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 284 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 345 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 456 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 484 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 545 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 656 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 684 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 745 LIES ON A SPECIAL POSITION. 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 MET B 1 REMARK 465 MET C 1 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 ARG A 128 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 128 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 128 CG CD NE CZ NH1 NH2 DBREF 1QU9 A 2 128 UNP P39330 YJGF_ECOLI 1 127 DBREF 1QU9 B 2 128 UNP P39330 YJGF_ECOLI 1 127 DBREF 1QU9 C 2 128 UNP P39330 YJGF_ECOLI 1 127 SEQADV 1QU9 MET A 1 UNP P39330 CONFLICT SEQADV 1QU9 CSP A 107 UNP P39330 CYS 106 MODIFIED RESIDUE SEQADV 1QU9 MET B 1 UNP P39330 CONFLICT SEQADV 1QU9 CSP B 107 UNP P39330 CYS 106 MODIFIED RESIDUE SEQADV 1QU9 MET C 1 UNP P39330 CONFLICT SEQADV 1QU9 CSP C 107 UNP P39330 CYS 106 MODIFIED RESIDUE SEQRES 1 A 128 MET SER LYS THR ILE ALA THR GLU ASN ALA PRO ALA ALA SEQRES 2 A 128 ILE GLY PRO TYR VAL GLN GLY VAL ASP LEU GLY ASN MET SEQRES 3 A 128 ILE ILE THR SER GLY GLN ILE PRO VAL ASN PRO LYS THR SEQRES 4 A 128 GLY GLU VAL PRO ALA ASP VAL ALA ALA GLN ALA ARG GLN SEQRES 5 A 128 SER LEU ASP ASN VAL LYS ALA ILE VAL GLU ALA ALA GLY SEQRES 6 A 128 LEU LYS VAL GLY ASP ILE VAL LYS THR THR VAL PHE VAL SEQRES 7 A 128 LYS ASP LEU ASN ASP PHE ALA THR VAL ASN ALA THR TYR SEQRES 8 A 128 GLU ALA PHE PHE THR GLU HIS ASN ALA THR PHE PRO ALA SEQRES 9 A 128 ARG SER CSP VAL GLU VAL ALA ARG LEU PRO LYS ASP VAL SEQRES 10 A 128 LYS ILE GLU ILE GLU ALA ILE ALA VAL ARG ARG SEQRES 1 B 128 MET SER LYS THR ILE ALA THR GLU ASN ALA PRO ALA ALA SEQRES 2 B 128 ILE GLY PRO TYR VAL GLN GLY VAL ASP LEU GLY ASN MET SEQRES 3 B 128 ILE ILE THR SER GLY GLN ILE PRO VAL ASN PRO LYS THR SEQRES 4 B 128 GLY GLU VAL PRO ALA ASP VAL ALA ALA GLN ALA ARG GLN SEQRES 5 B 128 SER LEU ASP ASN VAL LYS ALA ILE VAL GLU ALA ALA GLY SEQRES 6 B 128 LEU LYS VAL GLY ASP ILE VAL LYS THR THR VAL PHE VAL SEQRES 7 B 128 LYS ASP LEU ASN ASP PHE ALA THR VAL ASN ALA THR TYR SEQRES 8 B 128 GLU ALA PHE PHE THR GLU HIS ASN ALA THR PHE PRO ALA SEQRES 9 B 128 ARG SER CSP VAL GLU VAL ALA ARG LEU PRO LYS ASP VAL SEQRES 10 B 128 LYS ILE GLU ILE GLU ALA ILE ALA VAL ARG ARG SEQRES 1 C 128 MET SER LYS THR ILE ALA THR GLU ASN ALA PRO ALA ALA SEQRES 2 C 128 ILE GLY PRO TYR VAL GLN GLY VAL ASP LEU GLY ASN MET SEQRES 3 C 128 ILE ILE THR SER GLY GLN ILE PRO VAL ASN PRO LYS THR SEQRES 4 C 128 GLY GLU VAL PRO ALA ASP VAL ALA ALA GLN ALA ARG GLN SEQRES 5 C 128 SER LEU ASP ASN VAL LYS ALA ILE VAL GLU ALA ALA GLY SEQRES 6 C 128 LEU LYS VAL GLY ASP ILE VAL LYS THR THR VAL PHE VAL SEQRES 7 C 128 LYS ASP LEU ASN ASP PHE ALA THR VAL ASN ALA THR TYR SEQRES 8 C 128 GLU ALA PHE PHE THR GLU HIS ASN ALA THR PHE PRO ALA SEQRES 9 C 128 ARG SER CSP VAL GLU VAL ALA ARG LEU PRO LYS ASP VAL SEQRES 10 C 128 LYS ILE GLU ILE GLU ALA ILE ALA VAL ARG ARG MODRES 1QU9 CSP A 107 CYS S-PHOSPHOCYSTEINE MODRES 1QU9 CSP B 107 CYS S-PHOSPHOCYSTEINE MODRES 1QU9 CSP C 107 CYS S-PHOSPHOCYSTEINE HET CSP A 107 12 HET CSP B 107 12 HET CSP C 107 12 HETNAM CSP S-PHOSPHOCYSTEINE FORMUL 1 CSP 3(C3 H8 N O5 P S) FORMUL 4 HOH *474(H2 O) HELIX 1 1 ASP A 45 ALA A 64 1 20 HELIX 2 2 LYS A 67 GLY A 69 5 3 HELIX 3 3 ASP A 80 ASN A 82 5 3 HELIX 4 4 ASP A 83 HIS A 98 1 16 HELIX 5 5 LEU A 113 VAL A 117 5 5 HELIX 6 6 ASP B 45 ALA B 64 1 20 HELIX 7 7 LYS B 67 GLY B 69 5 3 HELIX 8 8 ASP B 80 ASN B 82 5 3 HELIX 9 9 ASP B 83 HIS B 98 1 16 HELIX 10 10 LEU B 113 VAL B 117 5 5 HELIX 11 11 ASP C 45 ALA C 64 1 20 HELIX 12 12 LYS C 67 GLY C 69 5 3 HELIX 13 13 ASP C 80 ASN C 82 5 3 HELIX 14 14 ASP C 83 HIS C 98 1 16 HELIX 15 15 LEU C 113 VAL C 117 5 5 SHEET 1 A 6 LYS A 3 ILE A 5 0 SHEET 2 A 6 GLY A 20 ASP A 22 -1 O GLY A 20 N ILE A 5 SHEET 3 A 6 MET A 26 THR A 29 -1 O ILE A 28 N VAL A 21 SHEET 4 A 6 ILE A 119 VAL A 126 -1 O ALA A 123 N THR A 29 SHEET 5 A 6 ILE A 71 VAL A 78 -1 N VAL A 72 O ILE A 124 SHEET 6 A 6 ALA A 104 GLU A 109 1 N ALA A 104 O VAL A 72 SHEET 1 B 6 LYS B 3 ILE B 5 0 SHEET 2 B 6 GLY B 20 ASP B 22 -1 O GLY B 20 N ILE B 5 SHEET 3 B 6 MET B 26 THR B 29 -1 O ILE B 28 N VAL B 21 SHEET 4 B 6 ILE B 119 VAL B 126 -1 O ALA B 123 N THR B 29 SHEET 5 B 6 ILE B 71 VAL B 78 -1 N VAL B 72 O ILE B 124 SHEET 6 B 6 ALA B 104 GLU B 109 1 N ALA B 104 O VAL B 72 SHEET 1 C 6 LYS C 3 ILE C 5 0 SHEET 2 C 6 GLY C 20 ASP C 22 -1 O GLY C 20 N ILE C 5 SHEET 3 C 6 MET C 26 THR C 29 -1 O ILE C 28 N VAL C 21 SHEET 4 C 6 ILE C 119 VAL C 126 -1 O ALA C 123 N THR C 29 SHEET 5 C 6 ILE C 71 VAL C 78 -1 N VAL C 72 O ILE C 124 SHEET 6 C 6 ALA C 104 GLU C 109 1 N ALA C 104 O VAL C 72 LINK C SER A 106 N CSP A 107 1555 1555 1.33 LINK C CSP A 107 N VAL A 108 1555 1555 1.31 LINK C SER B 106 N CSP B 107 1555 1555 1.33 LINK C CSP B 107 N VAL B 108 1555 1555 1.31 LINK C SER C 106 N CSP C 107 1555 1555 1.33 LINK C CSP C 107 N VAL C 108 1555 1555 1.31 CRYST1 72.220 72.220 72.220 90.00 90.00 90.00 P 2 2 2 12 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 0.013847 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013847 0.00000