HEADER ANTIMICROBIAL PROTEIN 12-DEC-01 1KLL 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; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: COMPLEXED WITH 2,7-DIAMINOMITOSENE, RESIDUE 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 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 4 27-OCT-21 1KLL 1 REMARK SEQADV LINK 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,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 (%) : 99.6 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 : 1000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015083. 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 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 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. = -3.9 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 MUTATION SEQADV 1KLL MSE A 25 UNP O05205 LEU 25 ENGINEERED MUTATION 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-DIOXO- HETSYN 2 MC 2,3,4,7-TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN-8- HETSYN 3 MC 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