HEADER HYDROLASE 02-FEB-17 5UPG TITLE CRYSTAL STRUCTURE OF LPXC FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TITLE 2 PF-5081090 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDP-3-O-ACYL-GLCNAC DEACETYLASE,UDP-3-O-[R-3- COMPND 5 HYDROXYMYRISTOYL]-N-ACETYLGLUCOSAMINE DEACETYLASE, COMPND 6 PSAEA.00166.A.DG15; COMPND 7 EC: 3.5.1.108; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / DSM SOURCE 3 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1); SOURCE 4 ORGANISM_TAXID: 208964; SOURCE 5 STRAIN: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 SOURCE 6 / 1C / PRS 101 / PAO1; SOURCE 7 GENE: LPXC; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SSGCID, LPXC, UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE, PF- KEYWDS 2 5081090, LIPID A BIOSYNTHESIS, STRUCTURAL GENOMICS, SEATTLE KEYWDS 3 STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 2 04-OCT-23 5UPG 1 REMARK REVDAT 1 29-MAR-17 5UPG 0 JRNL AUTH J.N.PHAN,S.L.DELKER,D.D.LORIMER,T.E.EDWARDS JRNL TITL CRYSTAL STRUCTURE OF LPXC FROM PSEUDOMONAS AERUGINOSA IN JRNL TITL 2 COMPLEX WITH PF-5081090 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 28779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2043 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 40.9221 - 4.1916 1.00 1814 149 0.1338 0.1573 REMARK 3 2 4.1916 - 3.3274 1.00 1802 152 0.1233 0.1455 REMARK 3 3 3.3274 - 2.9070 1.00 1804 151 0.1357 0.1708 REMARK 3 4 2.9070 - 2.6412 1.00 1832 117 0.1455 0.1639 REMARK 3 5 2.6412 - 2.4519 1.00 1816 146 0.1511 0.1948 REMARK 3 6 2.4519 - 2.3074 1.00 1813 141 0.1451 0.2161 REMARK 3 7 2.3074 - 2.1918 1.00 1799 155 0.1476 0.1932 REMARK 3 8 2.1918 - 2.0964 1.00 1804 145 0.1386 0.1823 REMARK 3 9 2.0964 - 2.0157 1.00 1801 146 0.1437 0.1924 REMARK 3 10 2.0157 - 1.9462 1.00 1847 142 0.1573 0.2004 REMARK 3 11 1.9462 - 1.8853 0.99 1784 113 0.1596 0.1922 REMARK 3 12 1.8853 - 1.8314 0.97 1783 127 0.1629 0.2044 REMARK 3 13 1.8314 - 1.7832 0.96 1716 127 0.1805 0.2532 REMARK 3 14 1.7832 - 1.7397 0.93 1695 130 0.1961 0.2838 REMARK 3 15 1.7397 - 1.7002 0.89 1626 102 0.2310 0.2767 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.34 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 : 0.006 2632 REMARK 3 ANGLE : 0.868 3594 REMARK 3 CHIRALITY : 0.055 403 REMARK 3 PLANARITY : 0.005 462 REMARK 3 DIHEDRAL : 19.692 1609 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.8561 6.4602 -10.9396 REMARK 3 T TENSOR REMARK 3 T11: 0.0548 T22: 0.0605 REMARK 3 T33: 0.0618 T12: -0.0013 REMARK 3 T13: 0.0094 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.1471 L22: 1.1727 REMARK 3 L33: 0.5808 L12: -0.3155 REMARK 3 L13: 0.1848 L23: 0.3456 REMARK 3 S TENSOR REMARK 3 S11: 0.0361 S12: 0.0425 S13: -0.0163 REMARK 3 S21: -0.0694 S22: -0.1082 S23: 0.0590 REMARK 3 S31: -0.0554 S32: -0.0624 S33: 0.0662 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8334 9.9096 -3.5512 REMARK 3 T TENSOR REMARK 3 T11: 0.0658 T22: 0.0742 REMARK 3 T33: 0.0722 T12: -0.0218 REMARK 3 T13: -0.0041 T23: 0.0136 REMARK 3 L TENSOR REMARK 3 L11: 3.2658 L22: 2.8844 REMARK 3 L33: 2.6786 L12: 0.0791 REMARK 3 L13: -0.9990 L23: -1.2949 REMARK 3 S TENSOR REMARK 3 S11: 0.0658 S12: -0.0660 S13: 0.0954 REMARK 3 S21: 0.1690 S22: -0.0707 S23: -0.2143 REMARK 3 S31: -0.1973 S32: 0.3830 S33: -0.0076 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.0756 3.6583 -4.5376 REMARK 3 T TENSOR REMARK 3 T11: 0.0426 T22: 0.0493 REMARK 3 T33: 0.0353 T12: 0.0079 REMARK 3 T13: -0.0011 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.2567 L22: 1.4300 REMARK 3 L33: 0.4703 L12: 0.0254 REMARK 3 L13: -0.0378 L23: 0.2887 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: 0.0250 S13: 0.0015 REMARK 3 S21: -0.0685 S22: -0.0598 S23: -0.0317 REMARK 3 S31: -0.0256 S32: -0.0026 S33: 0.0393 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 147 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4840 -9.3727 -0.2158 REMARK 3 T TENSOR REMARK 3 T11: 0.0434 T22: 0.0282 REMARK 3 T33: 0.0423 T12: -0.0124 REMARK 3 T13: 0.0256 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.8821 L22: 0.7798 REMARK 3 L33: 1.9010 L12: -0.3053 REMARK 3 L13: 1.0957 L23: 0.2253 REMARK 3 S TENSOR REMARK 3 S11: 0.0892 S12: 0.0481 S13: -0.0722 REMARK 3 S21: 0.0205 S22: 0.0195 S23: -0.0619 REMARK 3 S31: 0.1140 S32: 0.1317 S33: -0.1096 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 148 THROUGH 170 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0298 -5.3340 16.5785 REMARK 3 T TENSOR REMARK 3 T11: 0.0599 T22: 0.0961 REMARK 3 T33: 0.0535 T12: -0.0044 REMARK 3 T13: -0.0101 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.4318 L22: 1.9006 REMARK 3 L33: 2.3700 L12: -0.8040 REMARK 3 L13: -1.0185 L23: 1.6491 REMARK 3 S TENSOR REMARK 3 S11: -0.0653 S12: -0.1115 S13: -0.0001 REMARK 3 S21: 0.2111 S22: 0.1233 S23: -0.0744 REMARK 3 S31: 0.1963 S32: 0.1564 S33: -0.0677 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 171 THROUGH 249 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3899 3.8693 11.8308 REMARK 3 T TENSOR REMARK 3 T11: 0.0401 T22: 0.0633 REMARK 3 T33: 0.0489 T12: -0.0080 REMARK 3 T13: -0.0071 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.4379 L22: 1.0167 REMARK 3 L33: 1.1212 L12: -0.0586 REMARK 3 L13: -0.0856 L23: 0.0839 REMARK 3 S TENSOR REMARK 3 S11: -0.0013 S12: -0.0329 S13: -0.0083 REMARK 3 S21: 0.0638 S22: -0.0409 S23: 0.0611 REMARK 3 S31: -0.0657 S32: -0.0222 S33: 0.0427 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 250 THROUGH 299 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7800 -9.7833 -1.5772 REMARK 3 T TENSOR REMARK 3 T11: 0.0574 T22: 0.0526 REMARK 3 T33: 0.0608 T12: 0.0086 REMARK 3 T13: 0.0032 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 1.3878 L22: 0.7226 REMARK 3 L33: 1.0665 L12: 0.7641 REMARK 3 L13: 1.0072 L23: 0.6549 REMARK 3 S TENSOR REMARK 3 S11: 0.0483 S12: 0.0487 S13: -0.0312 REMARK 3 S21: -0.0075 S22: -0.0075 S23: -0.0364 REMARK 3 S31: 0.0535 S32: -0.0167 S33: -0.0373 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 5UPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28780 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 7.242 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.29 REMARK 200 R MERGE FOR SHELL (I) : 0.53900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.380 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: 3UHM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES HCL, PH 7.7, 50MM CACL2, REMARK 280 4% (W/V) PROPANOL, 25% (W/V) PEG 3350, REMARK 280 PSAEA.00166.A.DG15.PD00471 AT 5MG/ML + 1MM ZNCL2 + 1MM BSI REMARK 280 101565 (PF-5081090), CRYO: 20% EG: TRAY 285924G10, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 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 ALA A 300 REMARK 465 ALA A 301 REMARK 465 ALA A 302 REMARK 465 VAL A 303 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 GLU A 59 CG CD OE1 OE2 REMARK 470 GLU A 287 CG CD OE1 OE2 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 ND2 ASN A 220 O HOH A 501 2.04 REMARK 500 O1 EDO A 408 O HOH A 502 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 530 O HOH A 798 1565 2.19 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 MET A 62 -2.45 68.05 REMARK 500 ALA A 91 148.18 -170.22 REMARK 500 MET A 103 -124.62 57.10 REMARK 500 ASP A 159 81.57 -154.14 REMARK 500 ASN A 220 16.76 -140.70 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 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 78 NE2 REMARK 620 2 HIS A 237 NE2 96.7 REMARK 620 3 ASP A 241 OD1 147.4 88.5 REMARK 620 4 ASP A 241 OD2 93.3 98.3 54.1 REMARK 620 5 8GJ A 401 O19 124.6 88.4 87.5 140.5 REMARK 620 6 8GJ A 401 O19 126.4 89.4 85.7 138.5 2.1 REMARK 620 7 8GJ A 401 O21 91.0 164.2 92.4 94.9 75.9 74.9 REMARK 620 8 8GJ A 401 O21 93.7 165.9 87.8 90.6 77.8 76.7 5.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 277 OD1 REMARK 620 2 ASP A 279 OD2 93.5 REMARK 620 3 8GJ A 402 N20 59.7 64.0 REMARK 620 4 8GJ A 402 O21 58.0 65.8 2.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8GJ A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8GJ A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SSGCID-PSAEA.00166.A RELATED DB: TARGETTRACK DBREF 5UPG A 1 303 UNP P47205 LPXC_PSEAE 1 303 SEQADV 5UPG SER A 0 UNP P47205 EXPRESSION TAG SEQRES 1 A 304 SER MET ILE LYS GLN ARG THR LEU LYS ASN ILE ILE ARG SEQRES 2 A 304 ALA THR GLY VAL GLY LEU HIS SER GLY GLU LYS VAL TYR SEQRES 3 A 304 LEU THR LEU LYS PRO ALA PRO VAL ASP THR GLY ILE VAL SEQRES 4 A 304 PHE CYS ARG THR ASP LEU ASP PRO VAL VAL GLU ILE PRO SEQRES 5 A 304 ALA ARG ALA GLU ASN VAL GLY GLU THR THR MET SER THR SEQRES 6 A 304 THR LEU VAL LYS GLY ASP VAL LYS VAL ASP THR VAL GLU SEQRES 7 A 304 HIS LEU LEU SER ALA MET ALA GLY LEU GLY ILE ASP ASN SEQRES 8 A 304 ALA TYR VAL GLU LEU SER ALA SER GLU VAL PRO ILE MET SEQRES 9 A 304 ASP GLY SER ALA GLY PRO PHE VAL PHE LEU ILE GLN SER SEQRES 10 A 304 ALA GLY LEU GLN GLU GLN GLU ALA ALA LYS LYS PHE ILE SEQRES 11 A 304 ARG ILE LYS ARG GLU VAL SER VAL GLU GLU GLY ASP LYS SEQRES 12 A 304 ARG ALA VAL PHE VAL PRO PHE ASP GLY PHE LYS VAL SER SEQRES 13 A 304 PHE GLU ILE ASP PHE ASP HIS PRO VAL PHE ARG GLY ARG SEQRES 14 A 304 THR GLN GLN ALA SER VAL ASP PHE SER SER THR SER PHE SEQRES 15 A 304 VAL LYS GLU VAL SER ARG ALA ARG THR PHE GLY PHE MET SEQRES 16 A 304 ARG ASP ILE GLU TYR LEU ARG SER GLN ASN LEU ALA LEU SEQRES 17 A 304 GLY GLY SER VAL GLU ASN ALA ILE VAL VAL ASP GLU ASN SEQRES 18 A 304 ARG VAL LEU ASN GLU ASP GLY LEU ARG TYR GLU ASP GLU SEQRES 19 A 304 PHE VAL LYS HIS LYS ILE LEU ASP ALA ILE GLY ASP LEU SEQRES 20 A 304 TYR LEU LEU GLY ASN SER LEU ILE GLY GLU PHE ARG GLY SEQRES 21 A 304 PHE LYS SER GLY HIS ALA LEU ASN ASN GLN LEU LEU ARG SEQRES 22 A 304 THR LEU ILE ALA ASP LYS ASP ALA TRP GLU VAL VAL THR SEQRES 23 A 304 PHE GLU ASP ALA ARG THR ALA PRO ILE SER TYR MET ARG SEQRES 24 A 304 PRO ALA ALA ALA VAL HET 8GJ A 401 56 HET 8GJ A 402 28 HET ZN A 403 1 HET ZN A 404 1 HET CL A 405 1 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HETNAM 8GJ (2R)-4-[4-(2-FLUORO-4-METHOXYPHENYL)-2-OXOPYRIDIN- HETNAM 2 8GJ 1(2H)-YL]-N-HYDROXY-2-METHYL-2-(METHYLSULFONYL) HETNAM 3 8GJ BUTANAMIDE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 8GJ 2(C18 H21 F N2 O6 S) FORMUL 4 ZN 2(ZN 2+) FORMUL 6 CL CL 1- FORMUL 7 EDO 6(C2 H6 O2) FORMUL 13 HOH *366(H2 O) HELIX 1 AA1 ARG A 53 GLU A 55 5 3 HELIX 2 AA2 VAL A 76 GLY A 87 1 12 HELIX 3 AA3 ALA A 107 GLY A 118 1 12 HELIX 4 AA4 SER A 180 VAL A 185 1 6 HELIX 5 AA5 ASP A 196 GLN A 203 1 8 HELIX 6 AA6 ASP A 232 TYR A 247 1 16 HELIX 7 AA7 LEU A 248 GLY A 250 5 3 HELIX 8 AA8 GLY A 263 ASP A 277 1 15 HELIX 9 AA9 ASP A 288 ALA A 292 5 5 SHEET 1 AA1 2 LYS A 3 LEU A 7 0 SHEET 2 AA1 2 LEU A 119 ALA A 125 -1 O GLN A 122 N GLN A 4 SHEET 1 AA2 5 ILE A 11 VAL A 16 0 SHEET 2 AA2 5 LYS A 23 LYS A 29 -1 O LEU A 26 N ALA A 13 SHEET 3 AA2 5 ALA A 91 LEU A 95 -1 O GLU A 94 N THR A 27 SHEET 4 AA2 5 ILE A 37 ARG A 41 1 N VAL A 38 O VAL A 93 SHEET 5 AA2 5 VAL A 48 PRO A 51 -1 O ILE A 50 N PHE A 39 SHEET 1 AA3 3 VAL A 57 GLU A 59 0 SHEET 2 AA3 3 THR A 65 LYS A 68 -1 O THR A 65 N GLY A 58 SHEET 3 AA3 3 VAL A 71 ASP A 74 -1 O VAL A 73 N LEU A 66 SHEET 1 AA4 5 VAL A 135 GLU A 139 0 SHEET 2 AA4 5 LYS A 142 VAL A 147 -1 O PHE A 146 N VAL A 135 SHEET 3 AA4 5 SER A 252 PHE A 260 -1 O PHE A 260 N ARG A 143 SHEET 4 AA4 5 PHE A 152 GLU A 157 1 N LYS A 153 O PHE A 257 SHEET 5 AA4 5 GLN A 171 ASP A 175 -1 O VAL A 174 N VAL A 154 SHEET 1 AA5 5 VAL A 135 GLU A 139 0 SHEET 2 AA5 5 LYS A 142 VAL A 147 -1 O PHE A 146 N VAL A 135 SHEET 3 AA5 5 SER A 252 PHE A 260 -1 O PHE A 260 N ARG A 143 SHEET 4 AA5 5 PHE A 128 ILE A 131 1 N ILE A 129 O SER A 252 SHEET 5 AA5 5 TRP A 281 VAL A 284 -1 O GLU A 282 N ARG A 130 SHEET 1 AA6 2 PHE A 191 PHE A 193 0 SHEET 2 AA6 2 ILE A 215 VAL A 217 1 O VAL A 217 N GLY A 192 LINK NE2 HIS A 78 ZN ZN A 403 1555 1555 2.10 LINK NE2 HIS A 237 ZN ZN A 403 1555 1555 2.11 LINK OD1 ASP A 241 ZN ZN A 403 1555 1555 2.64 LINK OD2 ASP A 241 ZN ZN A 403 1555 1555 2.09 LINK OD1 ASP A 277 ZN ZN A 404 1555 1555 1.83 LINK OD2 ASP A 279 ZN ZN A 404 1555 1555 1.94 LINK O19A8GJ A 401 ZN ZN A 403 1555 1555 2.11 LINK O19B8GJ A 401 ZN ZN A 403 1555 1555 2.06 LINK O21A8GJ A 401 ZN ZN A 403 1555 1555 2.16 LINK O21B8GJ A 401 ZN ZN A 403 1555 1555 2.16 LINK N20 8GJ A 402 ZN ZN A 404 1555 1455 2.69 LINK O21 8GJ A 402 ZN ZN A 404 1555 1455 1.94 CISPEP 1 ASP A 45 PRO A 46 0 -4.08 SITE 1 AC1 23 LEU A 18 HIS A 19 MET A 62 GLU A 77 SITE 2 AC1 23 HIS A 78 THR A 190 PHE A 191 GLY A 192 SITE 3 AC1 23 PHE A 193 ILE A 197 LEU A 200 GLY A 209 SITE 4 AC1 23 ALA A 214 VAL A 216 HIS A 237 LYS A 238 SITE 5 AC1 23 ASP A 241 HIS A 264 ZN A 403 HOH A 569 SITE 6 AC1 23 HOH A 672 HOH A 700 HOH A 702 SITE 1 AC2 19 ALA A 84 GLY A 85 ARG A 133 PHE A 152 SITE 2 AC2 19 PHE A 176 SER A 177 THR A 179 SER A 180 SITE 3 AC2 19 PHE A 181 LEU A 253 ASP A 277 ASP A 279 SITE 4 AC2 19 ILE A 294 SER A 295 TYR A 296 MET A 297 SITE 5 AC2 19 ZN A 404 CL A 405 HOH A 656 SITE 1 AC3 4 HIS A 78 HIS A 237 ASP A 241 8GJ A 401 SITE 1 AC4 4 ASP A 277 ASP A 279 8GJ A 402 CL A 405 SITE 1 AC5 6 ARG A 133 LYS A 183 ASP A 277 ASP A 279 SITE 2 AC5 6 8GJ A 402 ZN A 404 SITE 1 AC6 6 GLY A 108 VAL A 111 PHE A 112 SER A 186 SITE 2 AC6 6 THR A 273 HOH A 742 SITE 1 AC7 3 ASP A 150 ASN A 204 HOH A 551 SITE 1 AC8 8 HIS A 19 THR A 61 SER A 63 ASP A 74 SITE 2 AC8 8 LEU A 205 HOH A 502 HOH A 506 HOH A 642 SITE 1 AC9 6 GLU A 138 GLY A 140 LEU A 228 GLU A 231 SITE 2 AC9 6 HOH A 514 HOH A 548 SITE 1 AD1 5 GLU A 55 VAL A 57 VAL A 67 ARG A 272 SITE 2 AD1 5 HOH A 535 SITE 1 AD2 1 GLU A 49 CRYST1 35.840 47.400 48.150 111.27 109.12 98.12 P 1 1 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 0.027902 0.003981 0.012696 0.00000 SCALE2 0.000000 0.021311 0.010365 0.00000 SCALE3 0.000000 0.000000 0.024444 0.00000