HEADER ISOMERASE 28-FEB-02 1IU9 TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF ASPARTATE RACEMASE FROM TITLE 2 PYROCOCCUS HORIKOSHII OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTATE RACEMASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 EC: 5.1.1.13; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 GENE: PPH0670E; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23C KEYWDS ASPARTATE RACEMASE, C-TERMINAL DOMAIN, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.LIU,K.IWATA,M.YOHDA,K.MIKI REVDAT 5 03-APR-24 1IU9 1 REMARK REVDAT 4 27-DEC-23 1IU9 1 REMARK LINK REVDAT 3 13-JUL-11 1IU9 1 VERSN REVDAT 2 24-FEB-09 1IU9 1 VERSN REVDAT 1 09-SEP-03 1IU9 0 JRNL AUTH L.LIU,K.IWATA,M.YOHDA,K.MIKI JRNL TITL STRUCTURAL INSIGHT INTO GENE DUPLICATION, GENE FUSION AND JRNL TITL 2 DOMAIN SWAPPING IN THE EVOLUTION OF PLP-INDEPENDENT AMINO JRNL TITL 3 ACID RACEMASES JRNL REF FEBS LETT. V. 528 114 2002 JRNL REFN ISSN 0014-5793 JRNL PMID 12297289 JRNL DOI 10.1016/S0014-5793(02)03264-7 REMARK 2 REMARK 2 RESOLUTION. 2.04 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) : 2.04 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) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 6457 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) : 0.225 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 334 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 986 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 60 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 850 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.91000 REMARK 3 B22 (A**2) : -5.71000 REMARK 3 B33 (A**2) : 3.80000 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) : 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 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) : 1.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.200 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.270 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.380 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 52.76 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 1IU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000005282. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : A FIXED-EXIT DOUBLE CRYSTAL REMARK 200 MONOCHRAMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34023 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : 0.09800 REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.25200 REMARK 200 R SYM FOR SHELL (I) : 0.22600 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: C-TERMINAL DOMAIN IN THE INTACT STRUCTURE OF REMARK 200 ASPARTATE RACEMASE FROM PYROCOCCUS HORIKOSHII OT3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG8000, 0.10M MES, 0.2M CALCIUM REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.2K 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 18.41450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.68300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.66400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.68300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.41450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.66400 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 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 CA A 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 115 O REMARK 620 2 ASP A 204 OD2 149.4 REMARK 620 3 ASP A 204 OD1 157.0 51.8 REMARK 620 4 HOH A 243 O 77.6 132.3 80.5 REMARK 620 5 HOH A 244 O 83.7 85.0 92.5 97.9 REMARK 620 6 HOH A 245 O 105.2 89.1 77.7 80.3 170.2 REMARK 620 7 HOH A 256 O 75.6 81.7 126.6 138.6 109.8 77.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JFL RELATED DB: PDB REMARK 900 IJFL CONTAINS ENTIRE PROTEIN. DBREF 1IU9 A 103 213 UNP O58403 O58403_PYRHO 103 213 SEQRES 1 A 111 MET ILE GLU GLU THR ALA LYS LYS VAL LYS GLU LEU GLY SEQRES 2 A 111 PHE LYS LYS ALA GLY LEU LEU ALA THR THR GLY THR ILE SEQRES 3 A 111 VAL SER GLY VAL TYR GLU LYS GLU PHE SER LYS TYR GLY SEQRES 4 A 111 VAL GLU ILE MET THR PRO THR GLU ASP GLU GLN LYS ASP SEQRES 5 A 111 VAL MET ARG GLY ILE TYR GLU GLY VAL LYS ALA GLY ASN SEQRES 6 A 111 LEU LYS LEU GLY ARG GLU LEU LEU LEU LYS THR ALA LYS SEQRES 7 A 111 ILE LEU GLU GLU ARG GLY ALA GLU CYS ILE ILE ALA GLY SEQRES 8 A 111 CYS THR GLU VAL SER VAL VAL LEU LYS GLN ASP ASP LEU SEQRES 9 A 111 LYS VAL PRO LEU ILE ASP PRO HET CA A 1 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *56(H2 O) HELIX 1 1 MET A 103 LEU A 114 1 12 HELIX 2 2 THR A 124 GLY A 131 1 8 HELIX 3 3 GLY A 131 LYS A 139 1 9 HELIX 4 4 THR A 148 GLU A 161 1 14 HELIX 5 5 ASN A 167 ARG A 185 1 19 HELIX 6 6 CYS A 194 LEU A 201 1 8 HELIX 7 7 LYS A 202 LEU A 206 5 5 SHEET 1 A 4 GLU A 143 MET A 145 0 SHEET 2 A 4 LYS A 118 LEU A 122 1 N ALA A 119 O MET A 145 SHEET 3 A 4 ILE A 190 ALA A 192 1 O ILE A 191 N GLY A 120 SHEET 4 A 4 LEU A 210 ILE A 211 1 O ILE A 211 N ILE A 190 LINK CA CA A 1 O GLY A 115 1555 3545 2.36 LINK CA CA A 1 OD2 ASP A 204 1555 1555 2.38 LINK CA CA A 1 OD1 ASP A 204 1555 1555 2.62 LINK CA CA A 1 O HOH A 243 1555 1555 2.26 LINK CA CA A 1 O HOH A 244 1555 1555 2.42 LINK CA CA A 1 O HOH A 245 1555 1555 2.49 LINK CA CA A 1 O HOH A 256 1555 1555 2.51 SITE 1 AC1 6 GLY A 115 ASP A 204 HOH A 243 HOH A 244 SITE 2 AC1 6 HOH A 245 HOH A 256 CRYST1 36.829 45.328 57.366 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 0.027153 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017432 0.00000