HEADER LIPID BINDING PROTEIN,TRANSFERASE 31-OCT-05 2EVB TITLE STRUCTURE OF BIOTIN CARBOXYL CARRIER PROTEIN (74VAL START) FROM TITLE 2 PYROCOCCUS HORIKOSHI OT3 LIGAND FREE FORM I COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLMALONYL-COA DECARBOXYLASE GAMMA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 73-146; COMPND 5 SYNONYM: BIOTIN CARBOXYL CARRIER PROTEIN; COMPND 6 EC: 2.1.3.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 GENE: BCCP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET 11A KEYWDS BIOTIN, BCCP, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, LIPID BINDING PROTEIN, KEYWDS 4 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.BAGAUTDINOV,N.KUNISHIMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 4 25-OCT-23 2EVB 1 SEQADV REVDAT 3 13-JUL-11 2EVB 1 VERSN REVDAT 2 27-MAY-08 2EVB 1 JRNL VERSN REVDAT 1 01-MAY-06 2EVB 0 JRNL AUTH B.BAGAUTDINOV,Y.MATSUURA,S.BAGAUTDINOVA,N.KUNISHIMA JRNL TITL PROTEIN BIOTINYLATION VISUALIZED BY A COMPLEX STRUCTURE OF JRNL TITL 2 BIOTIN PROTEIN LIGASE WITH A SUBSTRATE JRNL REF J.BIOL.CHEM. V. 283 14739 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18372281 JRNL DOI 10.1074/JBC.M709116200 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.50 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) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 8821 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) : 0.248 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 469 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 : 2 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3220 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 28 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.062 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 556 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.45000 REMARK 3 B22 (A**2) : -8.24000 REMARK 3 B33 (A**2) : 1.78000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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: NULL REMARK 4 REMARK 4 2EVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.62 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8821 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 24.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.165 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1BDO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550 MME 55W/V(%), ACETATE, NAOH , REMARK 280 PH 4.62, MICROBATCH, TEMPERATURE 295K 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 13.53200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.84750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.76850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.84750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.53200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.76850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D5D RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN OTHER FORM REMARK 900 RELATED ID: PHO001001284.1 RELATED DB: TARGETDB DBREF 2EVB A 74 146 UNP O59021 O59021_PYRHO 77 149 SEQADV 2EVB MET A 73 UNP O59021 INITIATING METHIONINE SEQRES 1 A 74 MET VAL VAL SER GLU ASN VAL VAL SER ALA PRO MET PRO SEQRES 2 A 74 GLY LYS VAL LEU ARG VAL LEU VAL ARG VAL GLY ASP ARG SEQRES 3 A 74 VAL ARG VAL GLY GLN GLY LEU LEU VAL LEU GLU ALA MET SEQRES 4 A 74 LYS MET GLU ASN GLU ILE PRO SER PRO ARG ASP GLY VAL SEQRES 5 A 74 VAL LYS ARG ILE LEU VAL LYS GLU GLY GLU ALA VAL ASP SEQRES 6 A 74 THR GLY GLN PRO LEU ILE GLU LEU GLY FORMUL 2 HOH *111(H2 O) SHEET 1 A 4 VAL A 79 SER A 81 0 SHEET 2 A 4 PRO A 141 LEU A 145 -1 O ILE A 143 N VAL A 80 SHEET 3 A 4 GLY A 123 ILE A 128 -1 N ARG A 127 O GLU A 144 SHEET 4 A 4 ARG A 98 VAL A 99 -1 N VAL A 99 O GLY A 123 SHEET 1 B 4 MET A 113 PRO A 118 0 SHEET 2 B 4 GLY A 104 ALA A 110 -1 N LEU A 108 O ASN A 115 SHEET 3 B 4 GLY A 86 VAL A 91 -1 N LYS A 87 O GLU A 109 SHEET 4 B 4 ALA A 135 VAL A 136 -1 O VAL A 136 N GLY A 86 CRYST1 27.064 39.537 57.695 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 0.036949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017333 0.00000