PDB Short entry for 1MJM HEADER TRANSCRIPTION/DNA 30-JAN-98 1MJM TITLE METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE TITLE 2 CONSENSUS OPERATOR SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HALF CONSENSUS DNA OPERATOR DUPLEX; COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: METHIONINE REPRESSOR; COMPND 7 CHAIN: A, B; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 5 ORGANISM_TAXID: 562; SOURCE 6 GENE: METJ; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION REGULATION, METJ, METHIONINE REPRESSOR, SHEET-HELIX- KEYWDS 2 HELIX, S-ADENOSYL METHIONINE, DNA, COMPLEX (TRANSCRIPTION KEYWDS 3 REGULATION-DNA), TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.W.GARVIE,S.E.V.PHILLIPS REVDAT 6 02-AUG-23 1MJM 1 REMARK REVDAT 5 03-NOV-21 1MJM 1 SEQADV REVDAT 4 24-FEB-09 1MJM 1 VERSN REVDAT 3 01-APR-03 1MJM 1 JRNL REVDAT 2 16-AUG-01 1MJM 5 REVDAT 1 02-AUG-99 1MJM 0 JRNL AUTH C.W.GARVIE,S.E.PHILLIPS JRNL TITL DIRECT AND INDIRECT READOUT IN MUTANT MET REPRESSOR-OPERATOR JRNL TITL 2 COMPLEXES. JRNL REF STRUCTURE FOLD.DES. V. 8 905 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10986458 JRNL DOI 10.1016/S0969-2126(00)00182-9 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.860 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 13755 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) : 0.227 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 725 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 53.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 505 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 32 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.063 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1690 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.310 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) : 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : PARAMETER.ELEMENTS REMARK 3 PARAMETER FILE 4 : PARAMETER.ELEMENTS REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : TOPOLOGY.ELEMENTS REMARK 3 TOPOLOGY FILE 4 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1MJM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000175027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60504 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 25.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.07500 REMARK 200 R SYM FOR SHELL (I) : 0.21700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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: PDB ENTRY 1CMA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (10MG/ML) + DNA (3.8MG/ML) WAS REMARK 280 CRYSTALLISED FROM 8-14% P4000, 100MM CITRATE BUFFER, PH 5.0-6.0, REMARK 280 20% GLYCEROL, PH 7.0 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 19.98000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.98000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.00000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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 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 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 ASP A 82 75.56 -69.83 REMARK 500 GLU B 2 -54.52 -179.07 REMARK 500 GLU B 13 77.49 -33.77 REMARK 500 HIS B 14 -41.66 -158.94 REMARK 500 LYS B 17 -20.69 -171.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MJ2 RELATED DB: PDB REMARK 900 RELATED ID: 1MJO RELATED DB: PDB REMARK 900 RELATED ID: 1MJP RELATED DB: PDB REMARK 900 RELATED ID: 1MJQ RELATED DB: PDB DBREF 1MJM A 1 104 UNP P0A8U6 METJ_ECOLI 1 104 DBREF 1MJM B 1 104 UNP P0A8U6 METJ_ECOLI 1 104 DBREF 1MJM C 401 410 PDB 1MJM 1MJM 401 410 DBREF 1MJM D 411 420 PDB 1MJM 1MJM 411 420 SEQADV 1MJM LYS A 44 UNP P0A8U6 GLN 44 ENGINEERED MUTATION SEQADV 1MJM LYS B 44 UNP P0A8U6 GLN 44 ENGINEERED MUTATION SEQRES 1 C 10 DG DA DG DA DC DG DT DC DT DC SEQRES 1 D 10 DG DA DG DA DC DG DT DC DT DC SEQRES 1 A 104 ALA GLU TRP SER GLY GLU TYR ILE SER PRO TYR ALA GLU SEQRES 2 A 104 HIS GLY LYS LYS SER GLU GLN VAL LYS LYS ILE THR VAL SEQRES 3 A 104 SER ILE PRO LEU LYS VAL LEU LYS ILE LEU THR ASP GLU SEQRES 4 A 104 ARG THR ARG ARG LYS VAL ASN ASN LEU ARG HIS ALA THR SEQRES 5 A 104 ASN SER GLU LEU LEU CYS GLU ALA PHE LEU HIS ALA PHE SEQRES 6 A 104 THR GLY GLN PRO LEU PRO ASP ASP ALA ASP LEU ARG LYS SEQRES 7 A 104 GLU ARG SER ASP GLU ILE PRO GLU ALA ALA LYS GLU ILE SEQRES 8 A 104 MET ARG GLU MET GLY ILE ASN PRO GLU THR TRP GLU TYR SEQRES 1 B 104 ALA GLU TRP SER GLY GLU TYR ILE SER PRO TYR ALA GLU SEQRES 2 B 104 HIS GLY LYS LYS SER GLU GLN VAL LYS LYS ILE THR VAL SEQRES 3 B 104 SER ILE PRO LEU LYS VAL LEU LYS ILE LEU THR ASP GLU SEQRES 4 B 104 ARG THR ARG ARG LYS VAL ASN ASN LEU ARG HIS ALA THR SEQRES 5 B 104 ASN SER GLU LEU LEU CYS GLU ALA PHE LEU HIS ALA PHE SEQRES 6 B 104 THR GLY GLN PRO LEU PRO ASP ASP ALA ASP LEU ARG LYS SEQRES 7 B 104 GLU ARG SER ASP GLU ILE PRO GLU ALA ALA LYS GLU ILE SEQRES 8 B 104 MET ARG GLU MET GLY ILE ASN PRO GLU THR TRP GLU TYR FORMUL 5 HOH *177(H2 O) HELIX 1 AA LEU A 30 VAL A 45 1 16 HELIX 2 AB ASN A 53 THR A 66 1 14 HELIX 3 AC GLU A 86 GLU A 94 1 9 HELIX 4 BA LEU B 30 VAL B 45 1 16 HELIX 5 BB ASN B 53 THR B 66 1 14 HELIX 6 BC GLU B 86 MET B 95 1 10 SHEET 1 AS1 1 VAL A 21 ILE A 28 0 SHEET 1 BS2 1 VAL B 21 ILE B 28 0 CRYST1 39.960 64.000 114.470 90.00 90.00 90.00 P 21 21 21 8 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 0.025025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008736 0.00000