HEADER ANTIMICROBIAL PROTEIN 17-DEC-01 1KMZ TITLE MOLECULAR BASIS OF MITOMYCIN C RESICTANCE IN STREPTOMYCES: CRYSTAL TITLE 2 STRUCTURES OF THE MRD PROTEIN WITH AND WITHOUT A DRUG DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOMYCIN-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MRD; MITOMYCIN RESISTANCE PROTEIN D; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES LAVENDULAE; SOURCE 3 ORGANISM_TAXID: 1914; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL221(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PHIS PARALELL I KEYWDS MITOMYCIN C, ANTIBIOTIC RESISTANCE, SAD, ANOMALOUS DIFFRACTION, KEYWDS 2 DOMAIN SWAPPING, P-STAKING, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.W.MARTIN,Z.DAUTER,Y.DEVEDJIEV,P.SHEFFIELD,F.JELEN,M.HE,D.SHERMAN, AUTHOR 2 J.OTLEWSKI,Z.S.DEREWENDA,U.DEREWENDA REVDAT 5 16-AUG-23 1KMZ 1 REMARK REVDAT 4 13-JUL-11 1KMZ 1 VERSN REVDAT 3 24-FEB-09 1KMZ 1 VERSN REVDAT 2 01-APR-03 1KMZ 1 JRNL REVDAT 1 19-JUL-02 1KMZ 0 JRNL AUTH T.W.MARTIN,Z.DAUTER,Y.DEVEDJIEV,P.SHEFFIELD,F.JELEN,M.HE, JRNL AUTH 2 D.H.SHERMAN,J.OTLEWSKI,Z.S.DEREWENDA,U.DEREWENDA JRNL TITL MOLECULAR BASIS OF MITOMYCIN C RESISTANCE IN STREPTOMYCES: JRNL TITL 2 STRUCTURE AND FUNCTION OF THE MRD PROTEIN. JRNL REF STRUCTURE V. 10 933 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12121648 JRNL DOI 10.1016/S0969-2126(02)00778-5 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.163 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1478 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 16273 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.149 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 13491 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 982 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 1.800 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KMZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9700 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17820 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.150 REMARK 200 R MERGE (I) : 0.03400 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) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 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: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 1KLL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MES BUFFER, BETA REMARK 280 -OCTYLGLUCOSIDE, PH 6.0, VAPOR DIFFUSION AT 298K, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 22.25400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.32550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.25400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.32550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE CRYSTALLOGRAPHYC TWO FOLD AXIS 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 10.20973 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 30.32550 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 42.08650 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -12.04427 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 42.08650 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 SER A 2 REMARK 465 PRO A 67 REMARK 465 THR A 68 REMARK 465 GLY A 69 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 ASP A 44 CB CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2081 O HOH A 2142 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 7 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 ASP A 34 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 72 CA - CB - CG ANGL. DEV. = 21.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KLL RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH MITOMYCIN C DERIVATIVE DBREF 1KMZ A 1 130 UNP O05205 O05205_STRLA 1 130 SEQRES 1 A 130 MET SER ALA ARG ILE SER LEU PHE ALA VAL VAL VAL GLU SEQRES 2 A 130 ASP MET ALA LYS SER LEU GLU PHE TYR ARG LYS LEU GLY SEQRES 3 A 130 VAL GLU ILE PRO ALA GLU ALA ASP SER ALA PRO HIS THR SEQRES 4 A 130 GLU ALA VAL LEU ASP GLY GLY ILE ARG LEU ALA TRP ASP SEQRES 5 A 130 THR VAL GLU THR VAL ARG SER TYR ASP PRO GLU TRP GLN SEQRES 6 A 130 ALA PRO THR GLY GLY HIS ARG PHE ALA ILE ALA PHE GLU SEQRES 7 A 130 PHE PRO ASP THR ALA SER VAL ASP LYS LYS TYR ALA GLU SEQRES 8 A 130 LEU VAL ASP ALA GLY TYR GLU GLY HIS LEU LYS PRO TRP SEQRES 9 A 130 ASN ALA VAL TRP GLY GLN ARG TYR ALA ILE VAL LYS ASP SEQRES 10 A 130 PRO ASP GLY ASN VAL VAL ASP LEU PHE ALA PRO LEU PRO FORMUL 2 HOH *170(H2 O) HELIX 1 1 ASP A 14 LEU A 25 1 12 HELIX 2 2 GLU A 32 ALA A 36 5 5 HELIX 3 3 ASP A 44 GLY A 46 5 3 HELIX 4 4 VAL A 54 ASP A 61 1 8 HELIX 5 5 ASP A 81 ALA A 95 1 15 SHEET 1 A 7 HIS A 38 VAL A 42 0 SHEET 2 A 7 ARG A 48 THR A 53 -1 O LEU A 49 N ALA A 41 SHEET 3 A 7 ARG A 4 VAL A 12 1 N PHE A 8 O ALA A 50 SHEET 4 A 7 PHE A 73 GLU A 78 -1 O ALA A 76 N LEU A 7 SHEET 5 A 7 VAL A 122 PRO A 128 1 O ASP A 124 N PHE A 77 SHEET 6 A 7 GLN A 110 LYS A 116 -1 N ALA A 113 O LEU A 125 SHEET 7 A 7 GLU A 98 ASN A 105 -1 N GLU A 98 O LYS A 116 CRYST1 44.508 60.651 43.776 90.00 105.97 90.00 C 1 2 1 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 0.022468 0.000000 0.006430 0.00000 SCALE2 0.000000 0.016488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023761 0.00000