HEADER HYDROLASE 15-SEP-05 2B13 TITLE TRUNCATED S. AUREUS LYTM, P41 CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCYL-GLYCINE ENDOPEPTIDASE LYTM; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AUTOLYSIN LYTM; COMPND 5 EC: 3.4.24.75; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: LYTM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS LYTM, LYSOSTAPHIN, PEPTIDOGLYCAN AMIDASE, PEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.FIRCZUK,A.MUCHA,M.BOCHTLER REVDAT 5 23-AUG-23 2B13 1 REMARK LINK REVDAT 4 17-MAY-17 2B13 1 HETATM REVDAT 3 13-JUL-11 2B13 1 VERSN REVDAT 2 25-MAR-08 2B13 1 REMARK VERSN REVDAT 1 10-JAN-06 2B13 0 JRNL AUTH M.FIRCZUK,A.MUCHA,M.BOCHTLER JRNL TITL CRYSTAL STRUCTURES OF ACTIVE LYTM. JRNL REF J.MOL.BIOL. V. 354 578 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16269153 JRNL DOI 10.1016/J.JMB.2005.09.082 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.G.ODINTSOV,I.SABALA,M.MARCYJANIAK,M.BOCHTLER REMARK 1 TITL LATENT LYTM AT 1.3A RESOLUTION. REMARK 1 REF J.MOL.BIOL. V. 335 775 2004 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 14687573 REMARK 1 DOI 10.1016/J.JMB.2003.11.009 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 36606 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1940 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2579 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2004 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 342 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : 0.38000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.830 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2078 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1652 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2826 ; 1.480 ; 1.905 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3872 ; 3.994 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 260 ; 6.790 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 282 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2422 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 426 ; 0.009 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 384 ; 0.222 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1833 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1010 ; 0.115 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 214 ; 0.141 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.036 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 9 ; 0.107 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 39 ; 0.289 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.136 ; 0.200 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): 1284 ; 0.870 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2036 ; 1.511 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 794 ; 2.417 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 790 ; 3.779 ; 4.500 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): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 185 A 315 REMARK 3 ORIGIN FOR THE GROUP (A): -8.3540 26.0700 4.0160 REMARK 3 T TENSOR REMARK 3 T11: 0.0125 T22: 0.0396 REMARK 3 T33: 0.0026 T12: -0.0055 REMARK 3 T13: 0.0044 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.8514 L22: 0.4966 REMARK 3 L33: 0.3802 L12: 0.1165 REMARK 3 L13: 0.1192 L23: -0.0772 REMARK 3 S TENSOR REMARK 3 S11: 0.0035 S12: 0.0228 S13: 0.0382 REMARK 3 S21: -0.0342 S22: 0.0007 S23: -0.0164 REMARK 3 S31: 0.0210 S32: -0.0362 S33: -0.0042 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 185 B 315 REMARK 3 ORIGIN FOR THE GROUP (A): 20.9700 18.3960 15.9340 REMARK 3 T TENSOR REMARK 3 T11: 0.0282 T22: 0.0312 REMARK 3 T33: 0.0090 T12: 0.0019 REMARK 3 T13: -0.0055 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.2995 L22: 0.4638 REMARK 3 L33: 0.3648 L12: -0.1386 REMARK 3 L13: 0.0349 L23: 0.0608 REMARK 3 S TENSOR REMARK 3 S11: 0.0152 S12: -0.0217 S13: -0.0134 REMARK 3 S21: 0.0041 S22: 0.0009 S23: -0.0041 REMARK 3 S31: 0.0055 S32: -0.0139 S33: -0.0161 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 2B13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MAX-FLUX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38546 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 14.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.15200 REMARK 200 R SYM FOR SHELL (I) : 0.15200 REMARK 200 FOR SHELL : 10.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1QWY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG 8000, 0.2 M L(+)-TARTRATE, REMARK 280 0.1 M MES, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 31.48000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.74000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.22000 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 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 183 REMARK 465 ALA A 184 REMARK 465 ARG A 316 REMARK 465 MET B 183 REMARK 465 ALA B 184 REMARK 465 ARG B 316 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 ASN A 262 -120.88 -80.26 REMARK 500 ASP B 188 99.30 -161.43 REMARK 500 ALA B 234 114.42 -160.13 REMARK 500 ASN B 262 -125.93 -85.77 REMARK 500 SER B 283 41.09 -140.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 210 NE2 REMARK 620 2 ASP A 214 OD1 104.5 REMARK 620 3 ASP A 214 OD2 84.8 52.4 REMARK 620 4 HIS A 293 ND1 104.4 94.8 147.1 REMARK 620 5 TLA A 501 O41 148.1 90.5 82.5 102.1 REMARK 620 6 TLA A 501 O4 91.4 144.8 99.4 111.6 62.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 210 NE2 REMARK 620 2 ASP B 214 OD1 105.0 REMARK 620 3 HIS B 293 ND1 108.0 105.1 REMARK 620 4 TLA B 500 O4 92.1 128.8 114.9 REMARK 620 5 TLA B 500 O41 149.4 88.5 94.3 58.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLA B 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QWY RELATED DB: PDB REMARK 900 FULL-LENGTH LYTM REMARK 900 RELATED ID: 2B44 RELATED DB: PDB REMARK 900 TRUNCATED S. AUREUS LYTM, P 32 2 1 CRYSTAL FORM REMARK 900 RELATED ID: 2B0P RELATED DB: PDB REMARK 900 TRUNCATED S. AUREUS LYTM, P212121 CRYSTAL FORM DBREF 2B13 A 185 316 UNP O33599 LYTM_STAAU 185 316 DBREF 2B13 B 185 316 UNP O33599 LYTM_STAAU 185 316 SEQRES 1 A 134 MET ALA HIS ALA LYS ASP ALA SER TRP LEU THR SER ARG SEQRES 2 A 134 LYS GLN LEU GLN PRO TYR GLY GLN TYR HIS GLY GLY GLY SEQRES 3 A 134 ALA HIS TYR GLY VAL ASP TYR ALA MET PRO GLU ASN SER SEQRES 4 A 134 PRO VAL TYR SER LEU THR ASP GLY THR VAL VAL GLN ALA SEQRES 5 A 134 GLY TRP SER ASN TYR GLY GLY GLY ASN GLN VAL THR ILE SEQRES 6 A 134 LYS GLU ALA ASN SER ASN ASN TYR GLN TRP TYR MET HIS SEQRES 7 A 134 ASN ASN ARG LEU THR VAL SER ALA GLY ASP LYS VAL LYS SEQRES 8 A 134 ALA GLY ASP GLN ILE ALA TYR SER GLY SER THR GLY ASN SEQRES 9 A 134 SER THR ALA PRO HIS VAL HIS PHE GLN ARG MET SER GLY SEQRES 10 A 134 GLY ILE GLY ASN GLN TYR ALA VAL ASP PRO THR SER TYR SEQRES 11 A 134 LEU GLN SER ARG SEQRES 1 B 134 MET ALA HIS ALA LYS ASP ALA SER TRP LEU THR SER ARG SEQRES 2 B 134 LYS GLN LEU GLN PRO TYR GLY GLN TYR HIS GLY GLY GLY SEQRES 3 B 134 ALA HIS TYR GLY VAL ASP TYR ALA MET PRO GLU ASN SER SEQRES 4 B 134 PRO VAL TYR SER LEU THR ASP GLY THR VAL VAL GLN ALA SEQRES 5 B 134 GLY TRP SER ASN TYR GLY GLY GLY ASN GLN VAL THR ILE SEQRES 6 B 134 LYS GLU ALA ASN SER ASN ASN TYR GLN TRP TYR MET HIS SEQRES 7 B 134 ASN ASN ARG LEU THR VAL SER ALA GLY ASP LYS VAL LYS SEQRES 8 B 134 ALA GLY ASP GLN ILE ALA TYR SER GLY SER THR GLY ASN SEQRES 9 B 134 SER THR ALA PRO HIS VAL HIS PHE GLN ARG MET SER GLY SEQRES 10 B 134 GLY ILE GLY ASN GLN TYR ALA VAL ASP PRO THR SER TYR SEQRES 11 B 134 LEU GLN SER ARG HET ZN A 400 1 HET TLA A 501 10 HET ZN B 401 1 HET TLA B 500 10 HETNAM ZN ZINC ION HETNAM TLA L(+)-TARTARIC ACID FORMUL 3 ZN 2(ZN 2+) FORMUL 4 TLA 2(C4 H6 O6) FORMUL 7 HOH *342(H2 O) HELIX 1 1 ALA A 189 SER A 194 1 6 HELIX 2 2 GLY A 302 GLN A 304 5 3 HELIX 3 3 PRO A 309 GLN A 314 1 6 HELIX 4 4 ALA B 189 SER B 194 1 6 HELIX 5 5 GLY B 302 GLN B 304 5 3 HELIX 6 6 PRO B 309 GLN B 314 1 6 SHEET 1 A 7 GLN A 197 GLN A 199 0 SHEET 2 A 7 VAL A 213 ALA A 216 -1 O ASP A 214 N GLN A 199 SHEET 3 A 7 HIS A 291 SER A 298 -1 O PHE A 294 N VAL A 213 SHEET 4 A 7 ASN A 254 ASN A 261 -1 N TYR A 255 O MET A 297 SHEET 5 A 7 ASN A 243 GLU A 249 -1 N ILE A 247 O GLN A 256 SHEET 6 A 7 GLY A 229 TRP A 236 -1 N THR A 230 O LYS A 248 SHEET 7 A 7 LYS A 271 VAL A 272 -1 O VAL A 272 N GLY A 229 SHEET 1 B 4 GLN A 197 GLN A 199 0 SHEET 2 B 4 VAL A 213 ALA A 216 -1 O ASP A 214 N GLN A 199 SHEET 3 B 4 HIS A 291 SER A 298 -1 O PHE A 294 N VAL A 213 SHEET 4 B 4 ALA A 306 VAL A 307 -1 O VAL A 307 N ARG A 296 SHEET 1 C 2 GLY A 202 GLN A 203 0 SHEET 2 C 2 ALA A 209 HIS A 210 -1 O HIS A 210 N GLY A 202 SHEET 1 D 2 PRO A 222 TYR A 224 0 SHEET 2 D 2 GLN A 277 TYR A 280 -1 O ILE A 278 N VAL A 223 SHEET 1 E 7 GLN B 197 GLN B 199 0 SHEET 2 E 7 VAL B 213 ALA B 216 -1 O ASP B 214 N GLN B 199 SHEET 3 E 7 HIS B 291 SER B 298 -1 O PHE B 294 N VAL B 213 SHEET 4 E 7 ASN B 254 ASN B 261 -1 N TYR B 255 O MET B 297 SHEET 5 E 7 GLY B 242 GLU B 249 -1 N ILE B 247 O GLN B 256 SHEET 6 E 7 GLY B 229 SER B 237 -1 N THR B 230 O LYS B 248 SHEET 7 E 7 LYS B 271 VAL B 272 -1 O VAL B 272 N GLY B 229 SHEET 1 F 4 GLN B 197 GLN B 199 0 SHEET 2 F 4 VAL B 213 ALA B 216 -1 O ASP B 214 N GLN B 199 SHEET 3 F 4 HIS B 291 SER B 298 -1 O PHE B 294 N VAL B 213 SHEET 4 F 4 ALA B 306 VAL B 307 -1 O VAL B 307 N ARG B 296 SHEET 1 G 2 GLY B 202 GLN B 203 0 SHEET 2 G 2 ALA B 209 HIS B 210 -1 O HIS B 210 N GLY B 202 SHEET 1 H 2 PRO B 222 TYR B 224 0 SHEET 2 H 2 GLN B 277 TYR B 280 -1 O ILE B 278 N VAL B 223 LINK NE2 HIS A 210 ZN ZN A 400 1555 1555 2.08 LINK OD1 ASP A 214 ZN ZN A 400 1555 1555 2.10 LINK OD2 ASP A 214 ZN ZN A 400 1555 1555 2.65 LINK ND1 HIS A 293 ZN ZN A 400 1555 1555 2.08 LINK ZN ZN A 400 O41 TLA A 501 1555 1555 2.25 LINK ZN ZN A 400 O4 TLA A 501 1555 1555 2.18 LINK NE2 HIS B 210 ZN ZN B 401 1555 1555 2.07 LINK OD1 ASP B 214 ZN ZN B 401 1555 1555 1.97 LINK ND1 HIS B 293 ZN ZN B 401 1555 1555 2.05 LINK ZN ZN B 401 O4 TLA B 500 1555 1555 2.09 LINK ZN ZN B 401 O41 TLA B 500 1555 1555 2.39 SITE 1 AC2 4 HIS B 210 ASP B 214 HIS B 293 TLA B 500 SITE 1 AC3 13 HIS A 210 ASP A 214 HIS A 260 ASN A 286 SITE 2 AC3 13 SER A 287 THR A 288 HIS A 291 HIS A 293 SITE 3 AC3 13 HOH A 518 HOH A 544 HOH A 576 HOH A 581 SITE 4 AC3 13 HOH A 631 SITE 1 AC4 14 TYR B 204 HIS B 210 ASP B 214 HIS B 260 SITE 2 AC4 14 ASN B 286 SER B 287 THR B 288 HIS B 291 SITE 3 AC4 14 HIS B 293 ZN B 401 HOH B 529 HOH B 540 SITE 4 AC4 14 HOH B 544 HOH B 549 CRYST1 65.962 65.962 62.960 90.00 90.00 90.00 P 41 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 0.015160 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015883 0.00000