HEADER CELL CYCLE 25-OCT-18 6I0A TITLE CRYSTAL STRUCTURE OF RLPA SPOR DOMAIN FROM PSEUDOMONAS AERUGINOSA IN TITLE 2 COMPLEX WITH NUDED GLYCAN OBTAINED BY CO-CRYSTALLIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOLYTIC PEPTIDOGLYCAN TRANSGLYCOSYLASE RLPA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SPOR DOMAIN, UNP RESIDUES 265-342; COMPND 5 EC: 4.2.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: RLPA, PAMH19_1027; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYTIC TRANSGLYCOSYLASE, SEPTUM, SPOR DOMAIN, CELL DIVISION, DIVISOME, KEYWDS 2 MUREIN, DENUDED GLYCAN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR M.ALCORLO,J.A.HERMOSO REVDAT 4 24-JAN-24 6I0A 1 HETSYN LINK REVDAT 3 29-JUL-20 6I0A 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 27-MAY-20 6I0A 1 JRNL REVDAT 1 13-NOV-19 6I0A 0 JRNL AUTH M.ALCORLO,D.A.DIK,S.DE BENEDETTI,K.V.MAHASENAN,M.LEE, JRNL AUTH 2 T.DOMINGUEZ-GIL,D.HESEK,E.LASTOCHKIN,D.LOPEZ,B.BOGGESS, JRNL AUTH 3 S.MOBASHERY,J.A.HERMOSO JRNL TITL STRUCTURAL BASIS OF DENUDED GLYCAN RECOGNITION BY SPOR JRNL TITL 2 DOMAINS IN BACTERIAL CELL DIVISION. JRNL REF NAT COMMUN V. 10 5567 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31804467 JRNL DOI 10.1038/S41467-019-13354-4 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1072 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 48.0100 - 2.6000 1.00 2809 152 0.1635 0.1730 REMARK 3 2 2.6000 - 2.0600 1.00 2718 138 0.1794 0.2026 REMARK 3 3 2.0600 - 1.8000 1.00 2739 100 0.1561 0.2078 REMARK 3 4 1.8000 - 1.6400 1.00 2672 118 0.1588 0.2007 REMARK 3 5 1.6400 - 1.5200 1.00 2680 126 0.1506 0.1785 REMARK 3 6 1.5200 - 1.4300 0.99 2619 167 0.1798 0.2133 REMARK 3 7 1.4300 - 1.3600 0.99 2609 149 0.2103 0.2499 REMARK 3 8 1.3600 - 1.3000 0.99 2618 122 0.2366 0.2689 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.116 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.418 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.33 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 : 0.005 687 REMARK 3 ANGLE : 0.863 944 REMARK 3 CHIRALITY : 0.068 122 REMARK 3 PLANARITY : 0.004 120 REMARK 3 DIHEDRAL : 11.833 496 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 6I0A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012611. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-17 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) : 0.979257 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 272584 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 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: MOLREP REMARK 200 STARTING MODEL: 6I05 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M NAF AND 16% (W/V) PEG3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.54850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.54850 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.78350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.10950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.78350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.10950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.54850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.78350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.10950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 19.54850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.78350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.10950 REMARK 290 SMTRY3 8 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: MONOMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 523 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 584 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O4 NAG B 2 O5 AMU B 3 1.94 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6I0A A 266 342 UNP A0A0A8RDC6_PSEAI DBREF2 6I0A A A0A0A8RDC6 266 342 SEQRES 1 A 77 GLY LEU TYR LEU GLN VAL GLY ALA PHE ALA ASN PRO ASP SEQRES 2 A 77 ALA ALA GLU LEU LEU LYS ALA LYS LEU SER GLY VAL THR SEQRES 3 A 77 ALA ALA PRO VAL PHE ILE SER SER VAL VAL ARG ASN GLN SEQRES 4 A 77 GLN ILE LEU HIS ARG VAL ARG LEU GLY PRO ILE GLY SER SEQRES 5 A 77 ALA ASP GLU VAL SER ARG THR GLN ASP SER ILE ARG VAL SEQRES 6 A 77 ALA ASN LEU GLY GLN PRO THR LEU VAL ARG PRO ASP HET AMV B 1 21 HET NAG B 2 14 HET AMU B 3 19 HET NAG B 4 14 HETNAM AMV METHYL 2-ACETAMIDO-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY- HETNAM 2 AMV BETA-D-GLUCOPYRANOSIDE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM AMU N-ACETYL-BETA-MURAMIC ACID HETSYN AMV METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2- HETSYN 2 AMV DEOXY-BETA-D-GLUCOPYRANOSIDE; METHYL 2-ACETAMIDO-3-O- HETSYN 3 AMV [(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOSIDE; METHYL HETSYN 4 AMV 2-ACETAMIDO-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-D- HETSYN 5 AMV GLUCOSIDE; METHYL 2-ACETAMIDO-3-O-[(1R)-1- HETSYN 6 AMV CARBOXYETHYL]-2-DEOXY-GLUCOSIDE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN AMU N-ACETYL-MURAMIC ACID; BETA-N-ACETYLMURAMIC ACID FORMUL 2 AMV C12 H21 N O8 FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 AMU C11 H19 N O8 FORMUL 3 HOH *84(H2 O) HELIX 1 AA1 ASN A 276 GLY A 289 1 14 HELIX 2 AA2 SER A 317 ALA A 331 1 15 SHEET 1 AA1 4 VAL A 295 ARG A 302 0 SHEET 2 AA1 4 GLN A 305 ILE A 315 -1 O ARG A 311 N PHE A 296 SHEET 3 AA1 4 LEU A 267 PHE A 274 -1 N PHE A 274 O HIS A 308 SHEET 4 AA1 4 THR A 337 VAL A 339 -1 O THR A 337 N GLN A 270 LINK O4 AMV B 1 C1 NAG B 2 1555 1555 1.37 LINK O4 NAG B 2 C1 AMU B 3 1555 1555 1.37 LINK O4 AMU B 3 C1 NAG B 4 1555 1555 1.38 CISPEP 1 GLY A 313 PRO A 314 0 6.67 CRYST1 67.567 68.219 39.097 90.00 90.00 90.00 C 2 2 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 0.014800 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014659 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025577 0.00000