10 20 30 40 50 60 70 80 1SKF - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PENICILLIN-BINDING 20-AUG-98 1SKF
TITLE CRYSTAL STRUCTURE OF THE STREPTOMYCES K15 DD-TRANSPEPTIDASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANYL-D-ALANINE TRANSPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.16.4
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP.; SOURCE 3 ORGANISM_TAXID: 1958; SOURCE 4 STRAIN: K15
KEYWDS PENICILLIN-BINDING, DD-TRANSPEPTIDASE, SERINE PEPTIDASE, BETA- KEYWDS 2 LACTAMASE, HYDROLASE CARBOXYPEPTIDASE
EXPDTA X-RAY DIFFRACTION
AUTHOR E.FONZE,P.CHARLIER
REVDAT 4 13-JUL-11 1SKF 1 VERSN REVDAT 3 24-FEB-09 1SKF 1 VERSN REVDAT 2 01-APR-03 1SKF 1 JRNL REVDAT 1 20-AUG-99 1SKF 0
JRNL AUTH E.FONZE,M.VERMEIRE,M.NGUYEN-DISTECHE,R.BRASSEUR,P.CHARLIER JRNL TITL THE CRYSTAL STRUCTURE OF A PENICILLOYL-SERINE TRANSFERASE OF JRNL TITL 2 INTERMEDIATE PENICILLIN SENSITIVITY. THE DD-TRANSPEPTIDASE JRNL TITL 3 OF STREPTOMYCES K15. JRNL REF J.BIOL.CHEM. V. 274 21853 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 10419503 JRNL DOI 10.1074/JBC.274.31.21853
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.ENGLEBERT,P.CHARLIER,E.FONZE,Y.TO'TH,M.VERMEIRE, REMARK 1 AUTH 2 J.VAN BEEUMEN,J.GRANDCHAMPS,K.HOFFMANN,M.LEYH-BOUILLE, REMARK 1 AUTH 3 M.NGUYEN-DISTECHE,J.-M.GHUYSEN REMARK 1 TITL CRYSTALLIZATION AND X-RAY DIFFRACTION STUDY OF THE REMARK 1 TITL 2 STREPTOMYCES K15 PENICILLIN-BINDING DD-TRANSPEPTIDASE REMARK 1 REF J.MOL.BIOL. V. 241 295 1994 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 17859 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1776 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1322 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 138 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1927 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.67 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) : 1.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.950 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.390 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.980 ; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : TIP3P.PARAMETER REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TIP3P.TOPOLOGY REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1SKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.20 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23085 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 38.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.20
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 23.29650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.34850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.26400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.34850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.29650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.26400 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 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 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 386 O HOH A 441 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 25 101.77 -161.23 REMARK 500 ASN A 50 33.33 -96.18 REMARK 500 ASN A 71 55.64 39.15 REMARK 500 SER A 96 68.22 72.57 REMARK 500 SER A 152 -166.68 -166.00 REMARK 500 VAL A 212 -31.18 -138.37 REMARK 500 LYS A 213 134.35 178.36 REMARK 500 LYS A 221 -148.39 66.99 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 434 DISTANCE = 6.19 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: PENICILLIN-BINDING SITE
DBREF 1SKF A 1 262 UNP P39042 DACX_STRSK 30 291
SEQADV 1SKF ASN A 71 UNP P39042 LYS 100 CONFLICT SEQADV 1SKF ALA A 72 UNP P39042 PRO 101 CONFLICT SEQADV 1SKF THR A 113 UNP P39042 GLN 142 CONFLICT SEQADV 1SKF ARG A 114 UNP P39042 ALA 143 CONFLICT SEQADV 1SKF ASP A 156 UNP P39042 HIS 185 CONFLICT
SEQRES 1 A 262 VAL THR LYS PRO THR ILE ALA ALA VAL GLY GLY TYR ALA SEQRES 2 A 262 MET ASN ASN GLY THR GLY THR THR LEU TYR THR LYS ALA SEQRES 3 A 262 ALA ASP THR ARG ARG SER THR GLY SER THR THR LYS ILE SEQRES 4 A 262 MET THR ALA LYS VAL VAL LEU ALA GLN SER ASN LEU ASN SEQRES 5 A 262 LEU ASP ALA LYS VAL THR ILE GLN LYS ALA TYR SER ASP SEQRES 6 A 262 TYR VAL VAL ALA ASN ASN ALA SER GLN ALA HIS LEU ILE SEQRES 7 A 262 VAL GLY ASP LYS VAL THR VAL ARG GLN LEU LEU TYR GLY SEQRES 8 A 262 LEU MET LEU PRO SER GLY CYS ASP ALA ALA TYR ALA LEU SEQRES 9 A 262 ALA ASP LYS TYR GLY SER GLY SER THR ARG ALA ALA ARG SEQRES 10 A 262 VAL LYS SER PHE ILE GLY LYS MET ASN THR ALA ALA THR SEQRES 11 A 262 ASN LEU GLY LEU HIS ASN THR HIS PHE ASP SER PHE ASP SEQRES 12 A 262 GLY ILE GLY ASN GLY ALA ASN TYR SER THR PRO ARG ASP SEQRES 13 A 262 LEU THR LYS ILE ALA SER SER ALA MET LYS ASN SER THR SEQRES 14 A 262 PHE ARG THR VAL VAL LYS THR LYS ALA TYR THR ALA LYS SEQRES 15 A 262 THR VAL THR LYS THR GLY SER ILE ARG THR MET ASP THR SEQRES 16 A 262 TRP LYS ASN THR ASN GLY LEU LEU SER SER TYR SER GLY SEQRES 17 A 262 ALA ILE GLY VAL LYS THR GLY SER GLY PRO GLU ALA LYS SEQRES 18 A 262 TYR CYS LEU VAL PHE ALA ALA THR ARG GLY GLY LYS THR SEQRES 19 A 262 VAL ILE GLY THR VAL LEU ALA SER THR SER ILE PRO ALA SEQRES 20 A 262 ARG GLU SER ASP ALA THR LYS ILE MET ASN TYR GLY PHE SEQRES 21 A 262 ALA LEU
FORMUL 2 HOH *149(H2 O)
HELIX 1 1 GLY A 34 LEU A 46 5 13 HELIX 2 2 LYS A 61 ALA A 69 1 9 HELIX 3 3 VAL A 85 MET A 93 1 9 HELIX 4 4 CYS A 98 TYR A 108 1 11 HELIX 5 5 ARG A 114 LEU A 132 1 19 HELIX 6 6 PRO A 154 LYS A 166 1 13 HELIX 7 7 SER A 168 LYS A 175 1 8 HELIX 8 8 GLY A 201 SER A 205 5 5 HELIX 9 9 ILE A 245 PHE A 260 1 16
SHEET 1 A 5 ALA A 209 GLY A 217 0 SHEET 2 A 5 LYS A 221 ARG A 230 -1 N ALA A 227 O ILE A 210 SHEET 3 A 5 LYS A 233 LEU A 240 -1 N VAL A 239 O LEU A 224 SHEET 4 A 5 GLY A 10 ASN A 15 -1 N MET A 14 O ILE A 236 SHEET 5 A 5 THR A 21 LYS A 25 -1 N LYS A 25 O GLY A 11 SHEET 1 B 2 LYS A 56 THR A 58 0 SHEET 2 B 2 LYS A 82 THR A 84 -1 N VAL A 83 O VAL A 57 SHEET 1 C 2 LYS A 182 VAL A 184 0 SHEET 2 C 2 ILE A 190 THR A 192 -1 N ARG A 191 O THR A 183
CISPEP 1 GLY A 211 VAL A 212 0 -1.53
SITE 1 ACT 7 SER A 35 LYS A 38 SER A 96 CYS A 98 SITE 2 ACT 7 LYS A 213 THR A 214 GLY A 215
CRYST1 46.593 54.528 108.697 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 0.021462 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018339 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009200 0.00000