10 20 30 40 50 60 70 80 1KLL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIMICROBIAL PROTEIN 12-DEC-01 1KLL
TITLE MOLECULAR BASIS OF MITOMYCIN C RESICTANCE IN STREPTOMYCES: TITLE 2 CRYSTAL STRUCTURES OF THE MRD PROTEIN WITH AND WITHOUT A TITLE 3 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; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: COMPLEXED WITH 2,7-DIAMINOMITOSENE, RESIDUE COMPND 8 MC
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 KEYWDS 2 DIFFRACTION, CRYSTAL STRUCTURE, DOMAIN SWAPPING, P-STAKING, KEYWDS 3 ANTIMICROBIAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR T.W.MARTIN,Z.DAUTER,Y.DEVEDJIEV,P.SHEFFIELD,F.JELEN,M.HE, AUTHOR 2 D.SHERMAN,J.OTLEWSKI,Z.S.DEREWENDA,U.DEREWENDA
REVDAT 3 24-FEB-09 1KLL 1 VERSN REVDAT 2 01-APR-03 1KLL 1 JRNL REVDAT 1 19-JUL-02 1KLL 0
JRNL AUTH T.W.MARTIN,Z.DAUTER,Y.DEVEDJIEV,P.SHEFFIELD, JRNL AUTH 2 F.JELEN,M.HE,D.H.SHERMAN,J.OTLEWSKI,Z.S.DEREWENDA, JRNL AUTH 3 U.DEREWENDA JRNL TITL MOLECULAR BASIS OF MITOMYCIN C RESISTANCE IN JRNL TITL 2 STREPTOMYCES: STRUCTURE AND FUNCTION OF THE MRD JRNL TITL 3 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 1
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 (%) : 99.6 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) : 0.124 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1349 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18054 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)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL 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)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 153 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 : NULL 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) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 2.140 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 1KLL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-01. REMARK 100 THE RCSB ID CODE IS RCSB015083.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-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 : 18054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.640 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 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) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MES BUFFER, BETA- REMARK 280 OCTYLGLUCOSIDE, PH 6.0, VAPOR DIFFUSION, HANGING DROP AT 298K, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 22.37550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.22900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.37550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.22900 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE CRYSTALLOGRAPHIC 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 -12.72492 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 42.20022
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 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: 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 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MC A 9138
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KMZ RELATED DB: PDB REMARK 900 THE SAME UNCOMPLEXED PROTEIN
DBREF 1KLL A 1 130 UNP O05205 O05205_STRLA 1 130
SEQADV 1KLL MSE A 15 UNP O05205 MET 15 CLONING ARTIFACT SEQADV 1KLL MSE A 19 UNP O05205 LEU 19 ENGINEERED SEQADV 1KLL MSE A 25 UNP O05205 LEU 25 ENGINEERED
SEQRES 1 A 130 MET SER ALA ARG ILE SER LEU PHE ALA VAL VAL VAL GLU SEQRES 2 A 130 ASP MSE ALA LYS SER MSE GLU PHE TYR ARG LYS MSE 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
MODRES 1KLL MSE A 15 MET SELENOMETHIONINE MODRES 1KLL MSE A 19 MET SELENOMETHIONINE MODRES 1KLL MSE A 25 MET SELENOMETHIONINE
HET MSE A 15 17 HET MSE A 19 17 HET MSE A 25 17 HET MC A9138 37
HETNAM MSE SELENOMETHIONINE HETNAM MC 1,2-CIS-1-HYDROXY-2,7-DIAMINO-MITOSENE
HETSYN MC CARBAMIC ACID 2,6-DIAMINO-1-HYDROXY-5-METHYL-4,7- HETSYN 2 MC DIOXO-2,3,4,7-TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN- HETSYN 3 MC 8-YLMETHYL ESTER
FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 MC C14 H16 N4 O5 FORMUL 3 HOH *153(H2 O)
HELIX 1 1 ASP A 14 MSE 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 3 LEU A 7 VAL A 12 0 SHEET 2 A 3 ARG A 48 THR A 53 1 O ALA A 50 N PHE A 8 SHEET 3 A 3 HIS A 38 VAL A 42 -1 N ALA A 41 O LEU A 49 SHEET 1 B 4 ALA A 74 GLU A 78 0 SHEET 2 B 4 VAL A 122 PRO A 128 1 O ASP A 124 N PHE A 77 SHEET 3 B 4 GLN A 110 LYS A 116 -1 N VAL A 115 O VAL A 123 SHEET 4 B 4 GLU A 98 ASN A 105 -1 N TRP A 104 O TYR A 112
LINK C ASP A 14 N MSE A 15 1555 1555 1.33 LINK C MSE A 15 N ALA A 16 1555 1555 1.34 LINK C SER A 18 N MSE A 19 1555 1555 1.32 LINK C MSE A 19 N GLU A 20 1555 1555 1.34 LINK C LYS A 24 N MSE A 25 1555 1555 1.34 LINK C MSE A 25 N GLY A 26 1555 1555 1.34
SITE 1 AC1 13 HIS A 38 ASP A 52 THR A 56 TYR A 60 SITE 2 AC1 13 VAL A 107 TRP A 108 GLN A 110 TYR A 112 SITE 3 AC1 13 PHE A 126 HOH A9139 HOH A9173 HOH A9183 SITE 4 AC1 13 HOH A9226
CRYST1 44.751 60.458 44.077 90.00 106.78 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 0.022346 0.000000 0.006738 0.00000
SCALE2 0.000000 0.016540 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023697 0.00000