10 20 30 40 50 60 70 80 2DXA - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSLATION 25-AUG-06 2DXA
TITLE CRYSTAL STRUCTURE OF TRANS EDITING ENZYME PROX FROM E.COLI
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN YBAK; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE TRANS-EDITING ENZYME FOR PROLYL-TRNA COMPND 5 SYNTHETASE; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 5 EXPRESSION_SYSTEM_PLASMID: PX060110-16; SOURCE 6 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS TRANS-EDITING DOMAIN, PROLYL-TRNA SYNTHETASE, STRUCTURAL KEYWDS 2 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSLATION
EXPDTA X-RAY DIFFRACTION
AUTHOR M.KATO-MURAYAMA,K.MURAYAMA,T.TERADA,M.SHIROUZU,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 2DXA 1 VERSN REVDAT 1 25-FEB-07 2DXA 0
JRNL AUTH M.KATO-MURAYAMA,K.MURAYAMA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF TRANS EDITING ENZYME PROX JRNL TITL 2 FROM E.COLI JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 863450.900 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 20589 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) : 0.180 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2990 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 174 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1225 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 0.14000 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) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : -0.02 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.95 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.220 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.120 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 43.65 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2DXA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB025957.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFORCAL MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20627 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 32.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 50.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.09600 REMARK 200 <I/SIGMA(I)> 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 1DBX REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, TRIS, 10MM CYS-SA, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 20.84300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.97300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.90600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.97300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.84300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.90600 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: 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 GLY A -6 REMARK 465 SER A -5 REMARK 465 SER A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 ASP A 159
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1201
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ECO002000470.1 RELATED DB: TARGETDB
DBREF 2DXA A 1 159 UNP P0AAR3 YBAK_ECOLI 1 159
SEQADV 2DXA GLY A -6 UNP P0AAR3 CLONING ARTIFACT SEQADV 2DXA SER A -5 UNP P0AAR3 CLONING ARTIFACT SEQADV 2DXA SER A -4 UNP P0AAR3 CLONING ARTIFACT SEQADV 2DXA GLY A -3 UNP P0AAR3 CLONING ARTIFACT SEQADV 2DXA SER A -2 UNP P0AAR3 CLONING ARTIFACT SEQADV 2DXA SER A -1 UNP P0AAR3 CLONING ARTIFACT SEQADV 2DXA GLY A 0 UNP P0AAR3 CLONING ARTIFACT SEQADV 2DXA MSE A 1 UNP P0AAR3 MET 1 MODIFIED RESIDUE SEQADV 2DXA MSE A 56 UNP P0AAR3 MET 56 MODIFIED RESIDUE SEQADV 2DXA MSE A 86 UNP P0AAR3 MET 86 MODIFIED RESIDUE SEQADV 2DXA MSE A 90 UNP P0AAR3 MET 90 MODIFIED RESIDUE
SEQRES 1 A 166 GLY SER SER GLY SER SER GLY MSE THR PRO ALA VAL LYS SEQRES 2 A 166 LEU LEU GLU LYS ASN LYS ILE SER PHE GLN ILE HIS THR SEQRES 3 A 166 TYR GLU HIS ASP PRO ALA GLU THR ASN PHE GLY ASP GLU SEQRES 4 A 166 VAL VAL LYS LYS LEU GLY LEU ASN PRO ASP GLN VAL TYR SEQRES 5 A 166 LYS THR LEU LEU VAL ALA VAL ASN GLY ASP MSE LYS HIS SEQRES 6 A 166 LEU ALA VAL ALA VAL THR PRO VAL ALA GLY GLN LEU ASP SEQRES 7 A 166 LEU LYS LYS VAL ALA LYS ALA LEU GLY ALA LYS LYS VAL SEQRES 8 A 166 GLU MSE ALA ASP PRO MSE VAL ALA GLN ARG SER THR GLY SEQRES 9 A 166 TYR LEU VAL GLY GLY ILE SER PRO LEU GLY GLN LYS LYS SEQRES 10 A 166 ARG LEU PRO THR ILE ILE ASP ALA PRO ALA GLN GLU PHE SEQRES 11 A 166 ALA THR ILE TYR VAL SER GLY GLY LYS ARG GLY LEU ASP SEQRES 12 A 166 ILE GLU LEU ALA ALA GLY ASP LEU ALA LYS ILE LEU ASP SEQRES 13 A 166 ALA LYS PHE ALA ASP ILE ALA ARG ARG ASP
MODRES 2DXA MSE A 1 MET SELENOMETHIONINE MODRES 2DXA MSE A 56 MET SELENOMETHIONINE MODRES 2DXA MSE A 86 MET SELENOMETHIONINE MODRES 2DXA MSE A 90 MET SELENOMETHIONINE
HET MSE A 1 16 HET MSE A 56 16 HET MSE A 86 16 HET MSE A 90 8 HET CL A1201 1
HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION
FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 CL CL 1- FORMUL 3 HOH *283(H2 O)
HELIX 1 1 THR A 2 ASN A 11 1 10 HELIX 2 2 ASP A 31 GLY A 38 1 8 HELIX 3 3 ASP A 71 GLY A 80 1 10 HELIX 4 4 ASP A 88 GLY A 97 1 10 HELIX 5 5 PRO A 119 PHE A 123 5 5 HELIX 6 6 ALA A 140 ASP A 149 1 10
SHEET 1 A 5 GLN A 16 THR A 19 0 SHEET 2 A 5 LEU A 135 LEU A 139 -1 O GLU A 138 N GLN A 16 SHEET 3 A 5 ILE A 126 LYS A 132 -1 N VAL A 128 O ILE A 137 SHEET 4 A 5 VAL A 44 VAL A 52 1 N TYR A 45 O TYR A 127 SHEET 5 A 5 VAL A 84 MSE A 86 -1 O GLU A 85 N ALA A 51 SHEET 1 B 7 GLN A 16 THR A 19 0 SHEET 2 B 7 LEU A 135 LEU A 139 -1 O GLU A 138 N GLN A 16 SHEET 3 B 7 ILE A 126 LYS A 132 -1 N VAL A 128 O ILE A 137 SHEET 4 B 7 VAL A 44 VAL A 52 1 N TYR A 45 O TYR A 127 SHEET 5 B 7 ASP A 55 PRO A 65 -1 O HIS A 58 N VAL A 52 SHEET 6 B 7 THR A 114 ASP A 117 1 O ILE A 115 N VAL A 61 SHEET 7 B 7 LYS A 151 ALA A 153 1 O LYS A 151 N ILE A 116 SHEET 1 C 2 GLN A 69 LEU A 70 0 SHEET 2 C 2 ALA A 156 ARG A 157 -1 O ARG A 157 N GLN A 69
LINK C AMSE A 1 N THR A 2 1555 1555 1.33 LINK C BMSE A 1 N THR A 2 1555 1555 1.33 LINK C ASP A 55 N AMSE A 56 1555 1555 1.33 LINK C ASP A 55 N BMSE A 56 1555 1555 1.33 LINK C AMSE A 56 N LYS A 57 1555 1555 1.33 LINK C BMSE A 56 N LYS A 57 1555 1555 1.34 LINK C GLU A 85 N BMSE A 86 1555 1555 1.33 LINK C GLU A 85 N AMSE A 86 1555 1555 1.32 LINK C BMSE A 86 N ALA A 87 1555 1555 1.33 LINK C AMSE A 86 N ALA A 87 1555 1555 1.33 LINK C PRO A 89 N MSE A 90 1555 1555 1.33 LINK C MSE A 90 N VAL A 91 1555 1555 1.34
SITE 1 AC1 3 LEU A 70 LEU A 72 HOH A1397
CRYST1 41.686 53.812 65.946 90.00 90.00 90.00 P 21 21 21 4
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 0.023989 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018583 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015164 0.00000