HEADER LYASE 31-OCT-24 9KBQ TITLE CRYSTAL STRUCTURE OF PHAB10, A PEPTIDOGLYCAN HYDROLASE WITH THERMAL TITLE 2 STABILITY AND BROAD-SPECTRUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: FJU42_09780; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PEPTIDOGLYCAN DYDROLASE, CATIONIC PEPTIDES, DIMER, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR F.HU REVDAT 1 27-NOV-24 9KBQ 0 JRNL AUTH F.HU JRNL TITL CRYSTAL STRUCTURE OF PHAB10, A PEPTIDOGLYCAN HYDROLASE WITH JRNL TITL 2 THERMAL STABILITY AND BROAD-SPECTRUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 55215 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 2547 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.6500 - 3.9800 0.99 2970 152 0.1672 0.1789 REMARK 3 2 3.9800 - 3.1600 0.98 2969 129 0.1636 0.1771 REMARK 3 3 3.1600 - 2.7600 0.99 2957 151 0.1882 0.2038 REMARK 3 4 2.7600 - 2.5100 1.00 2966 136 0.1897 0.2310 REMARK 3 5 2.5100 - 2.3300 0.98 2932 123 0.1910 0.1961 REMARK 3 6 2.3300 - 2.1900 0.98 2864 165 0.1927 0.2484 REMARK 3 7 2.1900 - 2.0800 0.99 2956 144 0.1966 0.2375 REMARK 3 8 2.0800 - 1.9900 0.99 2862 159 0.1983 0.2247 REMARK 3 9 1.9900 - 1.9200 1.00 2979 145 0.2124 0.2155 REMARK 3 10 1.9200 - 1.8500 0.98 2903 152 0.2388 0.2980 REMARK 3 11 1.8500 - 1.7900 0.98 2908 123 0.2540 0.3100 REMARK 3 12 1.7900 - 1.7400 0.99 2929 133 0.2387 0.2925 REMARK 3 13 1.7400 - 1.6900 0.99 2938 138 0.0000 0.2375 REMARK 3 14 1.6900 - 1.6500 0.99 2942 131 0.2451 0.3080 REMARK 3 15 1.6500 - 1.6200 0.99 2945 143 0.2664 0.2874 REMARK 3 16 1.6200 - 1.5800 0.99 2926 132 0.2882 0.3581 REMARK 3 17 1.5800 - 1.5500 0.98 2844 154 0.3289 0.3640 REMARK 3 18 1.5500 - 1.5200 0.98 2878 137 0.3339 0.3749 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9KBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-APR-20. REMARK 100 THE DEPOSITION ID IS D_1300053241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 81 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55245 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 34.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 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 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: PHASES REMARK 200 STARTING MODEL: 1M38 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 3.5, 25% W/V REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 36.88500 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 21 REMARK 465 LYS A 169 REMARK 465 MET B 21 REMARK 465 LYS B 169 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASN A 122 NH2 ARG A 157 1655 2.11 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 PHE A 55 61.69 -107.34 REMARK 500 PHE B 55 65.57 -111.22 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9KBQ A 21 169 UNP A0A8B4M5Z7_ACIBA DBREF2 9KBQ A A0A8B4M5Z7 1 149 DBREF1 9KBQ B 21 169 UNP A0A8B4M5Z7_ACIBA DBREF2 9KBQ B A0A8B4M5Z7 1 149 SEQADV 9KBQ SER A 99 UNP A0A8B4M5Z PRO 79 CONFLICT SEQADV 9KBQ GLY A 132 UNP A0A8B4M5Z SER 112 CONFLICT SEQADV 9KBQ SER B 99 UNP A0A8B4M5Z PRO 79 CONFLICT SEQADV 9KBQ GLY B 132 UNP A0A8B4M5Z SER 112 CONFLICT SEQRES 1 A 149 MET SER LYS THR THR SER ASN ALA GLY LEU ASN LEU ILE SEQRES 2 A 149 LYS GLY PHE GLU GLY LYS ARG LEU ASN ALA TYR ASP ASP SEQRES 3 A 149 GLY VAL GLY VAL TRP THR ILE GLY PHE GLY THR ILE LYS SEQRES 4 A 149 TYR PRO ASN GLY VAL ARG VAL LYS LYS GLY ASP THR CYS SEQRES 5 A 149 THR GLU GLN GLN ALA GLU THR TYR LEU LYS ASN ASP LEU SEQRES 6 A 149 THR LYS PHE GLU VAL ALA ILE ASN LYS LEU VAL LYS VAL SEQRES 7 A 149 SER LEU THR GLN ASN GLN PHE ASP ALA LEU ALA SER PHE SEQRES 8 A 149 THR TYR ASN LEU GLY GLU THR ASN LEU ALA ASN SER THR SEQRES 9 A 149 LEU LEU LYS LYS LEU ASN LYS GLY ASP TYR GLN GLY ALA SEQRES 10 A 149 ALA ASP GLN PHE LEU VAL TRP ASN LYS ALA GLY GLY LYS SEQRES 11 A 149 VAL MET LYS GLY LEU VAL ARG ARG ARG GLU ALA GLU ARG SEQRES 12 A 149 ALA LEU PHE LEU LYS LYS SEQRES 1 B 149 MET SER LYS THR THR SER ASN ALA GLY LEU ASN LEU ILE SEQRES 2 B 149 LYS GLY PHE GLU GLY LYS ARG LEU ASN ALA TYR ASP ASP SEQRES 3 B 149 GLY VAL GLY VAL TRP THR ILE GLY PHE GLY THR ILE LYS SEQRES 4 B 149 TYR PRO ASN GLY VAL ARG VAL LYS LYS GLY ASP THR CYS SEQRES 5 B 149 THR GLU GLN GLN ALA GLU THR TYR LEU LYS ASN ASP LEU SEQRES 6 B 149 THR LYS PHE GLU VAL ALA ILE ASN LYS LEU VAL LYS VAL SEQRES 7 B 149 SER LEU THR GLN ASN GLN PHE ASP ALA LEU ALA SER PHE SEQRES 8 B 149 THR TYR ASN LEU GLY GLU THR ASN LEU ALA ASN SER THR SEQRES 9 B 149 LEU LEU LYS LYS LEU ASN LYS GLY ASP TYR GLN GLY ALA SEQRES 10 B 149 ALA ASP GLN PHE LEU VAL TRP ASN LYS ALA GLY GLY LYS SEQRES 11 B 149 VAL MET LYS GLY LEU VAL ARG ARG ARG GLU ALA GLU ARG SEQRES 12 B 149 ALA LEU PHE LEU LYS LYS FORMUL 3 HOH *260(H2 O) HELIX 1 AA1 SER A 26 GLY A 38 1 13 HELIX 2 AA2 THR A 73 LEU A 85 1 13 HELIX 3 AA3 LEU A 85 VAL A 96 1 12 HELIX 4 AA4 THR A 101 GLY A 116 1 16 HELIX 5 AA5 GLY A 116 ASN A 122 1 7 HELIX 6 AA6 SER A 123 LYS A 131 1 9 HELIX 7 AA7 ASP A 133 PHE A 141 1 9 HELIX 8 AA8 LEU A 142 TRP A 144 5 3 HELIX 9 AA9 MET A 152 LYS A 168 1 17 HELIX 10 AB1 SER B 26 GLY B 38 1 13 HELIX 11 AB2 THR B 73 VAL B 96 1 24 HELIX 12 AB3 THR B 101 GLY B 116 1 16 HELIX 13 AB4 GLY B 116 SER B 123 1 8 HELIX 14 AB5 SER B 123 LYS B 131 1 9 HELIX 15 AB6 ASP B 133 PHE B 141 1 9 HELIX 16 AB7 LEU B 142 TRP B 144 5 3 HELIX 17 AB8 MET B 152 LYS B 168 1 17 SHEET 1 AA1 2 ARG A 40 ASP A 45 0 SHEET 2 AA1 2 TRP A 51 GLY A 54 -1 O GLY A 54 N ARG A 40 SHEET 1 AA2 2 LYS A 146 ALA A 147 0 SHEET 2 AA2 2 LYS A 150 VAL A 151 -1 O LYS A 150 N ALA A 147 SHEET 1 AA3 2 ARG B 40 ASP B 45 0 SHEET 2 AA3 2 TRP B 51 GLY B 54 -1 O GLY B 54 N ARG B 40 SHEET 1 AA4 2 LYS B 146 ALA B 147 0 SHEET 2 AA4 2 LYS B 150 VAL B 151 -1 O LYS B 150 N ALA B 147 CRYST1 31.860 73.770 78.620 90.00 93.02 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 0.031387 0.000000 0.001656 0.00000 SCALE2 0.000000 0.013556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012737 0.00000