10 20 30 40 50 60 70 80 1PMD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PEPTIDOGLYCAN SYNTHESIS 05-FEB-96 1PMD
TITLE PENICILLIN-BINDING PROTEIN 2X (PBP-2X)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDOGLYCAN SYNTHESIS MULTIFUNCTIONAL ENZYME; COMPND 3 CHAIN: A
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313
KEYWDS PEPTIDOGLYCAN SYNTHESIS, RESISTANCE, CELL WALL, KEYWDS 2 TRANSMEMBRANE
EXPDTA X-RAY DIFFRACTION
MDLTYP CA ATOMS ONLY, CHAIN A
AUTHOR S.PARES,N.MOUZ,O.DIDEBERG
REVDAT 2 24-FEB-09 1PMD 1 VERSN REVDAT 1 05-FEB-97 1PMD 0
JRNL AUTH S.PARES,N.MOUZ,Y.PETILLOT,R.HAKENBECK,O.DIDEBERG JRNL TITL X-RAY STRUCTURE OF STREPTOCOCCUS PNEUMONIAE PBP2X, JRNL TITL 2 A PRIMARY PENICILLIN TARGET ENZYME. JRNL REF NAT.STRUCT.BIOL. V. 3 284 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8605631 JRNL DOI 10.1038/NSB0396-284
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.CHARLIER,G.BUISSON,O.DIDEBERG,J.WIERENGA,W.KECK, REMARK 1 AUTH 2 G.LAIBLE,R.HAKENBECK REMARK 1 TITL CRYSTALLIZATION OF A GENETICALLY ENGINEERED REMARK 1 TITL 2 WATER-SOLUBLE PRIMARY PENICILLIN TARGET ENZYME. REMARK 1 TITL 3 THE HIGH MOLECULAR MASS PBP2X OF STREPTOCOCCUS REMARK 1 TITL 4 PNEUMONIAE REMARK 1 REF J.MOL.BIOL. V. 232 1007 1993 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.3 REMARK 3 NUMBER OF REFLECTIONS : 12257 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 0.316 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5118 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.00 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1PMD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
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) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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 : 16436 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.93333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.86667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 85.40000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 142.33333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.46667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.93333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 113.86667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 142.33333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 85.40000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 28.46667 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
DBREF 1PMD A 76 750 UNP P14677 PBPX_STRPN 76 750
SEQRES 1 A 675 ARG GLY THR ILE TYR ASP ARG ASN GLY VAL PRO ILE ALA SEQRES 2 A 675 GLU ASP ALA THR SER TYR ASN VAL TYR ALA VAL ILE ASP SEQRES 3 A 675 GLU ASN TYR LYS SER ALA THR GLY LYS ILE LEU TYR VAL SEQRES 4 A 675 GLU LYS THR GLN PHE ASN LYS VAL ALA GLU VAL PHE HIS SEQRES 5 A 675 LYS TYR LEU ASP MET GLU GLU SER TYR VAL ARG GLU GLN SEQRES 6 A 675 LEU SER GLN PRO ASN LEU LYS GLN VAL SER PHE GLY ALA SEQRES 7 A 675 LYS GLY ASN GLY ILE THR TYR ALA ASN MET MET SER ILE SEQRES 8 A 675 LYS LYS GLU LEU GLU ALA ALA GLU VAL LYS GLY ILE ASP SEQRES 9 A 675 PHE THR THR SER PRO ASN ARG SER TYR PRO ASN GLY GLN SEQRES 10 A 675 PHE ALA SER SER PHE ILE GLY LEU ALA GLN LEU HIS GLU SEQRES 11 A 675 ASN GLU ASP GLY SER LYS SER LEU LEU GLY THR SER GLY SEQRES 12 A 675 MET GLU SER SER LEU ASN SER ILE LEU ALA GLY THR ASP SEQRES 13 A 675 GLY ILE ILE THR TYR GLU LYS ASP ARG LEU GLY ASN ILE SEQRES 14 A 675 VAL PRO GLY THR GLU GLN VAL SER GLN ARG THR MET ASP SEQRES 15 A 675 GLY LYS ASP VAL TYR THR THR ILE SER SER PRO LEU GLN SEQRES 16 A 675 SER PHE MET GLU THR GLN MET ASP ALA PHE GLN GLU LYS SEQRES 17 A 675 VAL LYS GLY LYS TYR MET THR ALA THR LEU VAL SER ALA SEQRES 18 A 675 LYS THR GLY GLU ILE LEU ALA THR THR GLN ARG PRO THR SEQRES 19 A 675 PHE ASP ALA ASP THR LYS GLU GLY ILE THR GLU ASP PHE SEQRES 20 A 675 VAL TRP ARG ASP ILE LEU TYR GLN SER ASN TYR GLU PRO SEQRES 21 A 675 GLY SER THR MET LYS VAL MET MET LEU ALA ALA ALA ILE SEQRES 22 A 675 ASP ASN ASN THR PHE PRO GLY GLY GLU VAL PHE ASN SER SEQRES 23 A 675 SER GLU LEU LYS ILE ALA ASP ALA THR ILE ARG ASP TRP SEQRES 24 A 675 ASP VAL ASN GLU GLY LEU THR GLY GLY ARG MET MET THR SEQRES 25 A 675 PHE SER GLN GLY PHE ALA HIS SER SER ASN VAL GLY MET SEQRES 26 A 675 THR LEU LEU GLU GLN LYS MET GLY ASP ALA THR TRP LEU SEQRES 27 A 675 ASP TYR LEU ASN ARG PHE LYS PHE GLY VAL PRO THR ARG SEQRES 28 A 675 PHE GLY LEU THR ASP GLU TYR ALA GLY GLN LEU PRO ALA SEQRES 29 A 675 ASP ASN ILE VAL ASN ILE ALA GLN SER SER PHE GLY GLN SEQRES 30 A 675 GLY ILE SER VAL THR GLN THR GLN MET ILE ARG ALA PHE SEQRES 31 A 675 THR ALA ILE ALA ASN ASP GLY VAL MET LEU GLU PRO LYS SEQRES 32 A 675 PHE ILE SER ALA ILE TYR ASP PRO ASN ASP GLN THR ALA SEQRES 33 A 675 ARG LYS SER GLN LYS GLU ILE VAL GLY ASN PRO VAL SER SEQRES 34 A 675 LYS ASP ALA ALA SER LEU THR ARG THR ASN MET VAL LEU SEQRES 35 A 675 VAL GLY THR ASP PRO VAL TYR GLY THR MET TYR ASN HIS SEQRES 36 A 675 SER THR GLY LYS PRO THR VAL THR VAL PRO GLY GLN ASN SEQRES 37 A 675 VAL ALA LEU LYS SER GLY THR ALA GLN ILE ALA ASP GLU SEQRES 38 A 675 LYS ASN GLY GLY TYR LEU VAL GLY LEU THR ASP TYR ILE SEQRES 39 A 675 PHE SER ALA VAL SER MET SER PRO ALA GLU ASN PRO ASP SEQRES 40 A 675 PHE ILE LEU TYR VAL THR VAL GLN GLN PRO GLU HIS TYR SEQRES 41 A 675 SER GLY ILE GLN LEU GLY GLU PHE ALA ASN PRO ILE LEU SEQRES 42 A 675 GLU ARG ALA SER ALA MET LYS ASP SER LEU ASN LEU GLN SEQRES 43 A 675 THR THR ALA LYS ALA LEU GLU GLN VAL SER GLN GLN SER SEQRES 44 A 675 PRO TYR PRO MET PRO SER VAL LYS ASP ILE SER PRO GLY SEQRES 45 A 675 ASP LEU ALA GLU GLU LEU ARG ARG ASN LEU VAL GLN PRO SEQRES 46 A 675 ILE VAL VAL GLY THR GLY THR LYS ILE LYS ASN SER SER SEQRES 47 A 675 ALA GLU GLU GLY LYS ASN LEU ALA PRO ASN GLN GLN VAL SEQRES 48 A 675 LEU ILE LEU SER ASP LYS ALA GLU GLU VAL PRO ASP MET SEQRES 49 A 675 TYR GLY TRP THR LYS GLU THR ALA GLU THR LEU ALA LYS SEQRES 50 A 675 TRP LEU ASN ILE GLU LEU GLU PHE GLN GLY SER GLY SER SEQRES 51 A 675 THR VAL GLN LYS GLN ASP VAL ARG ALA ASN THR ALA ILE SEQRES 52 A 675 LYS ASP ILE LYS LYS ILE THR LEU THR LEU GLY ASP
CRYST1 161.250 161.250 170.800 90.00 90.00 120.00 P 61 2 2 12
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 0.006202 0.003580 0.000000 0.00000
SCALE2 0.000000 0.007161 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005855 0.00000