HEADER LYASE 02-APR-22 7XFT TITLE MUCP PDZ2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ZINC METALLOPROTEASE PA3649; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ2 DOMAIN; COMPND 5 SYNONYM: MUCP; COMPND 6 EC: 3.4.24.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 GENE: PA3649; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS MUCP, ALGINATE BIOSYNTHESIS, PSEUDOMONAS AERUGINOSA PAO1, CRYSTAL KEYWDS 2 STRUCTURE., LYASE EXPDTA X-RAY DIFFRACTION AUTHOR X.LOU,S.LI,Q.ZHANG,M.BARTLAM REVDAT 2 29-NOV-23 7XFT 1 REMARK REVDAT 1 05-APR-23 7XFT 0 JRNL AUTH X.LOU,S.LI,Q.ZHANG,M.BARTLAM JRNL TITL MUCP PDZ2 DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 26685 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.410 REMARK 3 FREE R VALUE TEST SET COUNT : 1977 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 24.6600 - 2.9200 1.00 1903 151 0.1862 0.1994 REMARK 3 2 2.9200 - 2.3200 1.00 1835 148 0.1725 0.2056 REMARK 3 3 2.3200 - 2.0200 1.00 1806 143 0.1577 0.1557 REMARK 3 4 2.0200 - 1.8400 1.00 1811 146 0.1560 0.1819 REMARK 3 5 1.8400 - 1.7100 1.00 1779 142 0.1560 0.1792 REMARK 3 6 1.7100 - 1.6100 1.00 1771 142 0.1478 0.1669 REMARK 3 7 1.6100 - 1.5300 0.99 1788 142 0.1426 0.1670 REMARK 3 8 1.5300 - 1.4600 0.99 1764 140 0.1454 0.1943 REMARK 3 9 1.4600 - 1.4000 0.98 1746 140 0.1504 0.2088 REMARK 3 10 1.4000 - 1.3500 0.98 1722 137 0.1518 0.1975 REMARK 3 11 1.3500 - 1.3100 0.97 1729 138 0.1527 0.1761 REMARK 3 12 1.3100 - 1.2700 0.96 1699 138 0.1597 0.1949 REMARK 3 13 1.2700 - 1.2400 0.96 1707 138 0.1663 0.1990 REMARK 3 14 1.2400 - 1.2100 0.93 1648 132 0.1742 0.1842 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) : 0.113 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.46 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 : 0.008 646 REMARK 3 ANGLE : 0.969 872 REMARK 3 CHIRALITY : 0.084 99 REMARK 3 PLANARITY : 0.015 118 REMARK 3 DIHEDRAL : 6.532 94 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 7XFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300028734. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27025 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.200 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: 3ID2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 0.1M SODIUM ARSENATE, REMARK 280 0.2M THIAMINE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 25.18800 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 25.18800 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 24.65600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.65600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.18800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.65600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.33000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.18800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.65600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.33000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.0 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.37600 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 VAL A 306 REMARK 465 ALA A 307 REMARK 465 GLY A 308 REMARK 465 THR A 309 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 NA A 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 262 O REMARK 620 2 HOH A 531 O 113.2 REMARK 620 3 HOH A 571 O 132.6 112.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 273 OE1 REMARK 620 2 HOH A 514 O 104.8 REMARK 620 N 1 DBREF 7XFT A 222 309 UNP Q9HXY3 Y3649_PSEAE 222 309 SEQADV 7XFT GLY A 220 UNP Q9HXY3 EXPRESSION TAG SEQADV 7XFT SER A 221 UNP Q9HXY3 EXPRESSION TAG SEQRES 1 A 90 GLY SER LEU PRO PRO VAL LEU ALA GLU LEU ASP PRO LYS SEQRES 2 A 90 GLY PRO ALA GLN ALA ALA GLY LEU LYS LEU GLY ASP ARG SEQRES 3 A 90 LEU GLN SER ILE ASP GLY ILE ALA VAL ASP ASP TRP GLN SEQRES 4 A 90 GLN VAL VAL ASP SER VAL ARG ALA ARG PRO GLY GLN ARG SEQRES 5 A 90 VAL GLN LEU LYS VAL LEU ARG ASP GLY GLU VAL LEU ASP SEQRES 6 A 90 VAL ALA LEU GLU LEU ALA VAL ARG GLY GLU GLY LYS ALA SEQRES 7 A 90 ARG SER GLY TYR MET GLY ALA GLY VAL ALA GLY THR HET VAL A 401 16 HET NA A 402 1 HET NA A 403 1 HET NA A 404 1 HET NA A 405 1 HET NA A 406 1 HETNAM VAL VALINE HETNAM NA SODIUM ION FORMUL 2 VAL C5 H11 N O2 FORMUL 3 NA 5(NA 1+) FORMUL 8 HOH *134(H2 O) HELIX 1 AA1 GLY A 233 ALA A 238 1 6 HELIX 2 AA2 ASP A 256 ALA A 266 1 11 HELIX 3 AA3 GLU A 294 ARG A 298 5 5 SHEET 1 AA1 2 GLU A 228 LEU A 229 0 SHEET 2 AA1 2 ALA A 304 GLY A 305 -1 O GLY A 305 N GLU A 228 SHEET 1 AA2 4 ILE A 252 ALA A 253 0 SHEET 2 AA2 4 ARG A 245 ILE A 249 -1 N ILE A 249 O ILE A 252 SHEET 3 AA2 4 ARG A 271 ARG A 278 -1 O LYS A 275 N GLN A 247 SHEET 4 AA2 4 GLU A 281 GLU A 288 -1 O LEU A 283 N VAL A 276 SHEET 1 AA3 2 ALA A 290 ARG A 292 0 SHEET 2 AA3 2 SER A 299 TYR A 301 -1 O SER A 299 N ARG A 292 LINK O PRO A 234 NA NA A 405 1555 1555 2.86 LINK O ASP A 262 NA NA A 406 1555 1555 2.76 LINK OE1 GLN A 273 NA NA A 403 1555 1555 2.34 LINK NA NA A 402 O HOH A 586 1555 1555 3.16 LINK NA NA A 403 O HOH A 514 1555 3655 3.00 LINK NA NA A 404 O HOH A 628 1555 1555 2.95 LINK NA NA A 406 O HOH A 531 1555 8556 2.75 LINK NA NA A 406 O HOH A 571 1555 1555 2.87 CRYST1 49.312 70.660 50.376 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 0.020279 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014152 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019851 0.00000