HEADER HYDROLASE 05-APR-21 7O4C TITLE CRYSTAL STRUCTURE OF PASTA DOMAINS OF THE PENICILLIN-BINDING PROTEIN 1 TITLE 2 (PBP1) FROM STAPHYLOCOCCUS AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS COL; SOURCE 3 ORGANISM_TAXID: 93062; SOURCE 4 GENE: PBP1, SACOL1194; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CELL DIVISION, ANTIBIOTIC RESISTANCE, PEPTIDOGLYCAN SYNTHESIS, KEYWDS 2 TRANSPEPTIDASE, PENICILLIN-BINDING PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MARTINEZ CABALLERO,J.A.HERMOSO REVDAT 2 31-JAN-24 7O4C 1 REMARK REVDAT 1 03-NOV-21 7O4C 0 JRNL AUTH S.MARTINEZ-CABALLERO,K.V.MAHASENAN,C.KIM,R.MOLINA,R.FELTZER, JRNL AUTH 2 M.LEE,R.BOULEY,D.HESEK,J.F.FISHER,I.G.MUNOZ,M.CHANG, JRNL AUTH 3 S.MOBASHERY,J.A.HERMOSO JRNL TITL INTEGRATIVE STRUCTURAL BIOLOGY OF THE PENICILLIN-BINDING JRNL TITL 2 PROTEIN-1 FROM STAPHYLOCOCCUS AUREUS , AN ESSENTIAL JRNL TITL 3 COMPONENT OF THE DIVISOME MACHINERY. JRNL REF COMPUT STRUCT BIOTECHNOL J V. 19 5392 2021 JRNL REFN ESSN 2001-0370 JRNL PMID 34667534 JRNL DOI 10.1016/J.CSBJ.2021.09.018 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2399 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3216 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1774 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.05000 REMARK 3 B22 (A**2) : -0.99000 REMARK 3 B33 (A**2) : -0.06000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.069 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.456 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1907 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1872 ; 0.018 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2587 ; 1.613 ; 1.633 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4376 ; 1.689 ; 1.598 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 6.420 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;41.558 ;28.108 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 378 ;14.359 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 260 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2201 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 355 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3779 ;14.601 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7O4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292113573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46753 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 42.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68700 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5OAU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400 HEPES FREE ACID/SODIUM REMARK 280 HYDROXIDE PEG 3000 GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291.15K 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 19.98600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.21100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.28100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.21100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.98600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.28100 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 801 DBREF1 7O4C A 597 713 UNP A0A0H2WVW5_STAAC DBREF2 7O4C A A0A0H2WVW5 597 713 DBREF1 7O4C B 597 713 UNP A0A0H2WVW5_STAAC DBREF2 7O4C B A0A0H2WVW5 597 713 SEQRES 1 A 117 ALA GLU TYR SER LYS VAL PRO ASP VAL GLU GLY GLN ASP SEQRES 2 A 117 LYS GLN LYS ALA ILE ASP ASN VAL SER ALA LYS SER LEU SEQRES 3 A 117 GLU PRO VAL THR ILE GLY SER GLY THR GLN ILE LYS ALA SEQRES 4 A 117 GLN SER ILE LYS ALA GLY ASN LYS VAL LEU PRO HIS SER SEQRES 5 A 117 LYS VAL LEU LEU LEU THR ASP GLY ASP LEU THR MET PRO SEQRES 6 A 117 ASP MET SER GLY TRP THR LYS GLU ASP VAL ILE ALA PHE SEQRES 7 A 117 GLU ASN LEU THR ASN ILE LYS VAL ASN LEU LYS GLY SER SEQRES 8 A 117 GLY PHE VAL SER HIS GLN SER ILE SER LYS GLY GLN LYS SEQRES 9 A 117 LEU THR GLU LYS ASP LYS ILE ASP VAL GLU PHE SER SER SEQRES 1 B 117 ALA GLU TYR SER LYS VAL PRO ASP VAL GLU GLY GLN ASP SEQRES 2 B 117 LYS GLN LYS ALA ILE ASP ASN VAL SER ALA LYS SER LEU SEQRES 3 B 117 GLU PRO VAL THR ILE GLY SER GLY THR GLN ILE LYS ALA SEQRES 4 B 117 GLN SER ILE LYS ALA GLY ASN LYS VAL LEU PRO HIS SER SEQRES 5 B 117 LYS VAL LEU LEU LEU THR ASP GLY ASP LEU THR MET PRO SEQRES 6 B 117 ASP MET SER GLY TRP THR LYS GLU ASP VAL ILE ALA PHE SEQRES 7 B 117 GLU ASN LEU THR ASN ILE LYS VAL ASN LEU LYS GLY SER SEQRES 8 B 117 GLY PHE VAL SER HIS GLN SER ILE SER LYS GLY GLN LYS SEQRES 9 B 117 LEU THR GLU LYS ASP LYS ILE ASP VAL GLU PHE SER SER HET CL A 801 1 HETNAM CL CHLORIDE ION FORMUL 3 CL CL 1- FORMUL 4 HOH *166(H2 O) HELIX 1 AA1 ASP A 609 ALA A 619 1 11 HELIX 2 AA2 THR A 667 ASN A 679 1 13 HELIX 3 AA3 ASP B 609 LYS B 620 1 12 HELIX 4 AA4 THR B 667 ASN B 679 1 13 SHEET 1 AA1 2 SER A 600 LYS A 601 0 SHEET 2 AA1 2 LYS A 643 VAL A 644 -1 O VAL A 644 N SER A 600 SHEET 1 AA2 3 GLU A 623 ILE A 627 0 SHEET 2 AA2 3 LYS A 649 THR A 654 1 O THR A 654 N ILE A 627 SHEET 3 AA2 3 ILE A 633 GLN A 636 -1 N LYS A 634 O LEU A 653 SHEET 1 AA3 3 VAL A 682 LYS A 685 0 SHEET 2 AA3 3 ILE A 707 SER A 712 1 O PHE A 711 N LYS A 685 SHEET 3 AA3 3 PHE A 689 GLN A 693 -1 N SER A 691 O GLU A 710 SHEET 1 AA4 2 SER B 600 LYS B 601 0 SHEET 2 AA4 2 LYS B 643 VAL B 644 -1 O VAL B 644 N SER B 600 SHEET 1 AA5 3 GLU B 623 ILE B 627 0 SHEET 2 AA5 3 LYS B 649 THR B 654 1 O LEU B 652 N VAL B 625 SHEET 3 AA5 3 ILE B 633 GLN B 636 -1 N ALA B 635 O LEU B 653 SHEET 1 AA6 3 VAL B 682 GLY B 686 0 SHEET 2 AA6 3 ILE B 707 SER B 712 1 O ILE B 707 N ASN B 683 SHEET 3 AA6 3 PHE B 689 GLN B 693 -1 N PHE B 689 O SER B 712 SITE 1 AC1 2 HIS A 647 HOH B 808 CRYST1 39.972 80.562 90.422 90.00 90.00 90.00 P 21 21 21 8 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 0.025018 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011059 0.00000