HEADER HYDROLASE 22-JUN-14 4QPB TITLE CATALYTIC DOMAIN OF THE ANTIMICROBIAL PEPTIDASE LYSOSTAPHIN FROM TITLE 2 STAPHYLOCOCCUS SIMULANS CRYSTALLIZED IN THE ABSENCE OF PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOSTAPHIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 248-386; COMPND 5 SYNONYM: GLYCYL-GLYCINE ENDOPEPTIDASE; COMPND 6 EC: 3.4.24.75; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS SIMULANS; SOURCE 3 ORGANISM_TAXID: 1286; SOURCE 4 STRAIN: STAPHYLOCOCCUS SIMULANS BV. STAPHYLOLYTICUS; SOURCE 5 GENE: LSS, U66883.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS PEPTIDASE FAMILY M23, PEPTIDOGLYCAN AMIDASE, METALLOPEPTIDASE, KEYWDS 2 PEPTIDOGLYCAN, HYDROLASE, EXTRACELLULAR EXPDTA X-RAY DIFFRACTION AUTHOR I.SABALA,E.JAGIELSKA,P.T.BARDELANG,H.CZAPINSKA,S.O.DAHMS,J.A.SHARPE, AUTHOR 2 R.JAMES,M.E.THAN,N.R.THOMAS,M.BOCHTLER REVDAT 3 20-SEP-23 4QPB 1 REMARK SEQADV LINK REVDAT 2 01-OCT-14 4QPB 1 JRNL REVDAT 1 09-JUL-14 4QPB 0 JRNL AUTH I.SABALA,E.JAGIELSKA,P.T.BARDELANG,H.CZAPINSKA,S.O.DAHMS, JRNL AUTH 2 J.A.SHARPE,R.JAMES,M.E.THAN,N.R.THOMAS,M.BOCHTLER JRNL TITL CRYSTAL STRUCTURE OF THE ANTIMICROBIAL PEPTIDASE LYSOSTAPHIN JRNL TITL 2 FROM STAPHYLOCOCCUS SIMULANS. JRNL REF FEBS J. V. 281 4112 2014 JRNL REFN ISSN 1742-464X JRNL PMID 25039253 JRNL DOI 10.1111/FEBS.12929 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 23387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN RESOLUTION SHELLS REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 707 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) : 1.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3304 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2082 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.36000 REMARK 3 B22 (A**2) : 1.61000 REMARK 3 B33 (A**2) : -0.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.161 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2214 ; 0.023 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1841 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3007 ; 1.754 ; 1.908 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4313 ; 1.388 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 6.904 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;32.937 ;24.272 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 334 ;13.202 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;22.563 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 287 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2566 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 0.013 ; 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): 1347 ; 1.043 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 580 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2152 ; 1.684 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 867 ; 2.679 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 855 ; 3.932 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4QPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000086342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : 23389 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 2.740 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16700 REMARK 200 FOR THE DATA SET : 7.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.73 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58600 REMARK 200 FOR SHELL : 2.100 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: PDB ENTRY 4QP5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6 MM PENTAPEPTIDE GGSGG, 0.1 M TRIS REMARK 280 (BASE), BICINE PH 8.5, 0.1 M AMINO ACIDS (L-NA-GLUTAMATE, REMARK 280 ALANINE (RACEMIC), GLYCINE; LYSINE-HCL (RACEMIC); SERINE REMARK 280 (RACEMIC)), 30% V/V PRECIPITANT (ETHYLENE GLYCOL, PEG 8000)., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 53.65900 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 247 REMARK 465 ALA A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 REMARK 465 HIS A 251 REMARK 465 ALA A 385 REMARK 465 GLY A 386 REMARK 465 MET B 247 REMARK 465 ALA B 248 REMARK 465 ALA B 249 REMARK 465 THR B 250 REMARK 465 ALA B 385 REMARK 465 GLY B 386 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 LYS B 336 CG CD CE NZ 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 ALA A 303 88.96 -155.81 REMARK 500 SER A 352 38.07 -144.15 REMARK 500 ASN A 368 -38.04 71.27 REMARK 500 ASN A 368 -40.16 72.35 REMARK 500 ALA B 303 86.13 -158.25 REMARK 500 SER B 352 41.74 -141.02 REMARK 500 ASN B 368 -21.51 82.84 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 279 NE2 REMARK 620 2 ASP A 283 OD1 98.7 REMARK 620 3 HIS A 362 ND1 100.3 101.2 REMARK 620 4 HOH A 530 O 80.4 103.5 154.9 REMARK 620 5 HOH A 595 O 91.3 168.6 82.3 72.7 REMARK 620 6 HOH A 598 O 151.8 91.0 103.7 71.6 77.6 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 279 NE2 REMARK 620 2 ASP B 283 OD1 100.0 REMARK 620 3 HIS B 362 ND1 101.1 102.7 REMARK 620 4 HOH B 614 O 87.9 169.9 81.6 REMARK 620 5 HOH B 616 O 140.4 99.6 107.6 70.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 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 EDO B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LXC RELATED DB: PDB REMARK 900 MATURE FORM OF THE ANTIMICROBIAL PEPTIDASE LYSOSTAPHIN FROM REMARK 900 STAPHYLOCOCCUS SIMULANS REMARK 900 RELATED ID: 4QP5 RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF THE ANTIMICROBIAL PEPTIDASE LYSOSTAPHIN FROM REMARK 900 STAPHYLOCOCCUS SIMULANS CRYSTALLIZED IN THE PRESENCE OF PHOSPHATE REMARK 900 RELATED ID: 1QWY RELATED DB: PDB REMARK 900 LATENT LYTM AT 1.3 A RESOLUTION REMARK 900 RELATED ID: 2B0P RELATED DB: PDB REMARK 900 TRUNCATED S. AUREUS LYTM, P212121 CRYSTAL FORM REMARK 900 RELATED ID: 2B13 RELATED DB: PDB REMARK 900 TRUNCATED S. AUREUS LYTM, P41 CRYSTAL FORM REMARK 900 RELATED ID: 2B44 RELATED DB: PDB REMARK 900 TRUNCATED S. AUREUS LYTM, P 32 2 1 CRYSTAL FORM REMARK 900 RELATED ID: 1R77 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CELL WALL TARGETING DOMAIN OF REMARK 900 PEPTIDYLGLYCAN HYDROLASE ALE-1 REMARK 900 RELATED ID: 3IT7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LASA VIRULENCE FACTOR FROM PSEUDOMONAS REMARK 900 AERUGINOSA REMARK 900 RELATED ID: 3IT5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LASA VIRULENCE FACTOR FROM PSEUDOMONAS REMARK 900 AERUGINOSA REMARK 900 RELATED ID: 4BH5 RELATED DB: PDB REMARK 900 LYTM DOMAIN OF ENVC, AN ACTIVATOR OF CELL WALL AMIDASES IN REMARK 900 ESCHERICHIA COLI DBREF 4QPB A 248 386 UNP P10547 LSTP_STASI 248 386 DBREF 4QPB B 248 386 UNP P10547 LSTP_STASI 248 386 SEQADV 4QPB MET A 247 UNP P10547 EXPRESSION TAG SEQADV 4QPB MET B 247 UNP P10547 EXPRESSION TAG SEQRES 1 A 140 MET ALA ALA THR HIS GLU HIS SER ALA GLN TRP LEU ASN SEQRES 2 A 140 ASN TYR LYS LYS GLY TYR GLY TYR GLY PRO TYR PRO LEU SEQRES 3 A 140 GLY ILE ASN GLY GLY MET HIS TYR GLY VAL ASP PHE PHE SEQRES 4 A 140 MET ASN ILE GLY THR PRO VAL LYS ALA ILE SER SER GLY SEQRES 5 A 140 LYS ILE VAL GLU ALA GLY TRP SER ASN TYR GLY GLY GLY SEQRES 6 A 140 ASN GLN ILE GLY LEU ILE GLU ASN ASP GLY VAL HIS ARG SEQRES 7 A 140 GLN TRP TYR MET HIS LEU SER LYS TYR ASN VAL LYS VAL SEQRES 8 A 140 GLY ASP TYR VAL LYS ALA GLY GLN ILE ILE GLY TRP SER SEQRES 9 A 140 GLY SER THR GLY TYR SER THR ALA PRO HIS LEU HIS PHE SEQRES 10 A 140 GLN ARG MET VAL ASN SER PHE SER ASN SER THR ALA GLN SEQRES 11 A 140 ASP PRO MET PRO PHE LEU LYS SER ALA GLY SEQRES 1 B 140 MET ALA ALA THR HIS GLU HIS SER ALA GLN TRP LEU ASN SEQRES 2 B 140 ASN TYR LYS LYS GLY TYR GLY TYR GLY PRO TYR PRO LEU SEQRES 3 B 140 GLY ILE ASN GLY GLY MET HIS TYR GLY VAL ASP PHE PHE SEQRES 4 B 140 MET ASN ILE GLY THR PRO VAL LYS ALA ILE SER SER GLY SEQRES 5 B 140 LYS ILE VAL GLU ALA GLY TRP SER ASN TYR GLY GLY GLY SEQRES 6 B 140 ASN GLN ILE GLY LEU ILE GLU ASN ASP GLY VAL HIS ARG SEQRES 7 B 140 GLN TRP TYR MET HIS LEU SER LYS TYR ASN VAL LYS VAL SEQRES 8 B 140 GLY ASP TYR VAL LYS ALA GLY GLN ILE ILE GLY TRP SER SEQRES 9 B 140 GLY SER THR GLY TYR SER THR ALA PRO HIS LEU HIS PHE SEQRES 10 B 140 GLN ARG MET VAL ASN SER PHE SER ASN SER THR ALA GLN SEQRES 11 B 140 ASP PRO MET PRO PHE LEU LYS SER ALA GLY HET ZN A 401 1 HET ZN B 401 1 HET EDO B 402 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *237(H2 O) HELIX 1 1 ALA A 255 TYR A 261 5 7 HELIX 2 2 GLY A 273 GLY A 276 5 4 HELIX 3 3 PRO A 378 LYS A 383 1 6 HELIX 4 4 ALA B 255 TYR B 261 5 7 HELIX 5 5 ILE B 274 GLY B 276 5 3 HELIX 6 6 PRO B 378 SER B 384 1 7 SHEET 1 A 2 GLY A 268 PRO A 269 0 SHEET 2 A 2 MET A 278 HIS A 279 -1 O HIS A 279 N GLY A 268 SHEET 1 B 6 VAL A 282 PHE A 285 0 SHEET 2 B 6 HIS A 360 VAL A 367 -1 O PHE A 363 N VAL A 282 SHEET 3 B 6 HIS A 323 LEU A 330 -1 N ARG A 324 O MET A 366 SHEET 4 B 6 GLY A 311 GLU A 318 -1 N LEU A 316 O GLN A 325 SHEET 5 B 6 GLY A 298 SER A 306 -1 N GLY A 304 O GLN A 313 SHEET 6 B 6 TYR A 340 VAL A 341 -1 O VAL A 341 N GLY A 298 SHEET 1 C 3 VAL A 282 PHE A 285 0 SHEET 2 C 3 HIS A 360 VAL A 367 -1 O PHE A 363 N VAL A 282 SHEET 3 C 3 ALA A 375 GLN A 376 -1 O GLN A 376 N ARG A 365 SHEET 1 D 3 PRO A 291 LYS A 293 0 SHEET 2 D 3 ILE A 346 TRP A 349 -1 O GLY A 348 N VAL A 292 SHEET 3 D 3 LYS A 332 TYR A 333 -1 N LYS A 332 O TRP A 349 SHEET 1 E 7 LYS B 262 LYS B 263 0 SHEET 2 E 7 VAL B 282 PHE B 285 -1 O PHE B 285 N LYS B 262 SHEET 3 E 7 HIS B 360 VAL B 367 -1 O LEU B 361 N PHE B 284 SHEET 4 E 7 HIS B 323 LEU B 330 -1 N TRP B 326 O GLN B 364 SHEET 5 E 7 GLY B 311 GLU B 318 -1 N GLU B 318 O HIS B 323 SHEET 6 E 7 GLY B 298 SER B 306 -1 N SER B 306 O GLY B 311 SHEET 7 E 7 TYR B 340 VAL B 341 -1 O VAL B 341 N GLY B 298 SHEET 1 F 4 LYS B 262 LYS B 263 0 SHEET 2 F 4 VAL B 282 PHE B 285 -1 O PHE B 285 N LYS B 262 SHEET 3 F 4 HIS B 360 VAL B 367 -1 O LEU B 361 N PHE B 284 SHEET 4 F 4 ALA B 375 GLN B 376 -1 O GLN B 376 N ARG B 365 SHEET 1 G 2 GLY B 268 PRO B 269 0 SHEET 2 G 2 MET B 278 HIS B 279 -1 O HIS B 279 N GLY B 268 SHEET 1 H 3 PRO B 291 LYS B 293 0 SHEET 2 H 3 ILE B 346 TRP B 349 -1 O GLY B 348 N VAL B 292 SHEET 3 H 3 LYS B 332 TYR B 333 -1 N LYS B 332 O TRP B 349 LINK NE2 HIS A 279 ZN ZN A 401 1555 1555 2.22 LINK OD1 ASP A 283 ZN ZN A 401 1555 1555 2.05 LINK ND1 HIS A 362 ZN ZN A 401 1555 1555 2.05 LINK ZN ZN A 401 O HOH A 530 1555 1555 2.65 LINK ZN ZN A 401 O HOH A 595 1555 1555 2.19 LINK ZN ZN A 401 O HOH A 598 1555 1555 2.16 LINK NE2 HIS B 279 ZN ZN B 401 1555 1555 2.27 LINK OD1 ASP B 283 ZN ZN B 401 1555 1555 2.09 LINK ND1 HIS B 362 ZN ZN B 401 1555 1555 2.12 LINK ZN ZN B 401 O HOH B 614 1555 1555 2.34 LINK ZN ZN B 401 O HOH B 616 1555 1555 2.38 SITE 1 AC1 6 HIS A 279 ASP A 283 HIS A 362 HOH A 530 SITE 2 AC1 6 HOH A 595 HOH A 598 SITE 1 AC2 5 HIS B 279 ASP B 283 HIS B 362 HOH B 614 SITE 2 AC2 5 HOH B 616 SITE 1 AC3 6 SER B 306 TYR B 308 GLY B 310 GLN B 313 SITE 2 AC3 6 TRP B 326 MET B 328 CRYST1 34.289 107.318 34.307 90.00 97.63 90.00 P 1 21 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 0.029164 0.000000 0.003905 0.00000 SCALE2 0.000000 0.009318 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029409 0.00000