HEADER HYDROLASE/HYDROLASE INHIBITOR 20-JUN-18 6DUI
TITLE CRYSTAL STRUCTURE OF LPXC FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH
TITLE 2 PT801
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PSAEA.00166.A.DG15;
COMPND 5 SYNONYM: UDP-3-O-ACYL-GLCNAC DEACETYLASE,UDP-3-O-[R-3-
COMPND 6 HYDROXYMYRISTOYL]-N-ACETYLGLUCOSAMINE DEACETYLASE;
COMPND 7 EC: 3.5.1.108;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA (STRAIN LESB58);
SOURCE 3 ORGANISM_TAXID: 557722;
SOURCE 4 STRAIN: LESB58;
SOURCE 5 GENE: LPXC, PLES_47851;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSAEA.00166.A.DG15
KEYWDS SSGCID, LPXC, LIPID A BIOSYNTHESIS, STRUCTURAL GENOMICS, SEATTLE
KEYWDS 2 STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, HYDROLASE-
KEYWDS 3 HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID)
REVDAT 2 11-OCT-23 6DUI 1 REMARK
REVDAT 1 26-JUN-19 6DUI 0
JRNL AUTH J.N.PHAN,S.L.DELKER,D.D.LORIMER,P.S.HORANYI,T.E.EDWARDS
JRNL TITL CRYSTAL STRUCTURE OF LPXC FROM PSEUDOMONAS AERUGINOSA IN
JRNL TITL 2 COMPLEX WITH PT801
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.14_3211: ???)
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) : 1.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.59
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8
REMARK 3 NUMBER OF REFLECTIONS : 37735
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.152
REMARK 3 R VALUE (WORKING SET) : 0.150
REMARK 3 FREE R VALUE : 0.188
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.390
REMARK 3 FREE R VALUE TEST SET COUNT : 2034
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 42.6014 - 3.8215 0.99 2468 119 0.1205 0.1482
REMARK 3 2 3.8215 - 3.0335 0.99 2401 158 0.1208 0.1614
REMARK 3 3 3.0335 - 2.6501 0.98 2408 153 0.1485 0.1790
REMARK 3 4 2.6501 - 2.4078 0.98 2393 138 0.1571 0.1918
REMARK 3 5 2.4078 - 2.2353 0.98 2429 144 0.1545 0.1937
REMARK 3 6 2.2353 - 2.1035 0.97 2353 147 0.1469 0.1950
REMARK 3 7 2.1035 - 1.9981 0.97 2409 120 0.1472 0.1654
REMARK 3 8 1.9981 - 1.9112 0.97 2403 125 0.1534 0.2254
REMARK 3 9 1.9112 - 1.8376 0.96 2399 117 0.1701 0.2196
REMARK 3 10 1.8376 - 1.7742 0.96 2339 139 0.1821 0.2327
REMARK 3 11 1.7742 - 1.7187 0.96 2375 118 0.1798 0.2154
REMARK 3 12 1.7187 - 1.6696 0.96 2367 147 0.1884 0.2281
REMARK 3 13 1.6696 - 1.6256 0.96 2341 127 0.1991 0.2803
REMARK 3 14 1.6256 - 1.5860 0.95 2324 151 0.2023 0.2257
REMARK 3 15 1.5860 - 1.5499 0.95 2292 131 0.2150 0.2506
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) : 0.150
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.630
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 12.64
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 2597
REMARK 3 ANGLE : 0.838 3550
REMARK 3 CHIRALITY : 0.056 405
REMARK 3 PLANARITY : 0.005 458
REMARK 3 DIHEDRAL : 19.310 1592
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 9
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 22 )
REMARK 3 ORIGIN FOR THE GROUP (A): -7.5766 2.9064 -10.4881
REMARK 3 T TENSOR
REMARK 3 T11: 0.0534 T22: 0.0967
REMARK 3 T33: 0.0539 T12: -0.0244
REMARK 3 T13: 0.0430 T23: 0.0449
REMARK 3 L TENSOR
REMARK 3 L11: 1.6508 L22: 4.4136
REMARK 3 L33: 2.7740 L12: -1.2170
REMARK 3 L13: 0.3342 L23: 2.2319
REMARK 3 S TENSOR
REMARK 3 S11: 0.0514 S12: 0.1104 S13: -0.0875
REMARK 3 S21: -0.2694 S22: -0.2166 S23: 0.3482
REMARK 3 S31: -0.1709 S32: -0.1789 S33: 0.1716
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 23 THROUGH 47 )
REMARK 3 ORIGIN FOR THE GROUP (A): -2.2199 9.5756 -14.3136
REMARK 3 T TENSOR
REMARK 3 T11: 0.1389 T22: 0.1200
REMARK 3 T33: 0.1120 T12: 0.0192
REMARK 3 T13: -0.0079 T23: 0.0516
REMARK 3 L TENSOR
REMARK 3 L11: 0.6678 L22: 1.1442
REMARK 3 L33: 0.4569 L12: 0.4265
REMARK 3 L13: 0.0317 L23: 0.5519
REMARK 3 S TENSOR
REMARK 3 S11: -0.0285 S12: 0.1790 S13: 0.1621
REMARK 3 S21: -0.1478 S22: -0.0084 S23: -0.0543
REMARK 3 S31: -0.0915 S32: -0.0554 S33: 0.0294
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 76 )
REMARK 3 ORIGIN FOR THE GROUP (A): 6.8994 9.8284 -4.1194
REMARK 3 T TENSOR
REMARK 3 T11: 0.0859 T22: 0.0823
REMARK 3 T33: 0.0992 T12: -0.0105
REMARK 3 T13: -0.0017 T23: 0.0236
REMARK 3 L TENSOR
REMARK 3 L11: 3.7938 L22: 4.3756
REMARK 3 L33: 4.5454 L12: 0.0948
REMARK 3 L13: -0.5179 L23: -1.2055
REMARK 3 S TENSOR
REMARK 3 S11: 0.0211 S12: -0.0627 S13: 0.2134
REMARK 3 S21: 0.1472 S22: 0.0064 S23: -0.1159
REMARK 3 S31: -0.2700 S32: 0.2296 S33: -0.0261
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 117 )
REMARK 3 ORIGIN FOR THE GROUP (A): -6.9601 3.5370 -6.0234
REMARK 3 T TENSOR
REMARK 3 T11: 0.1002 T22: 0.1111
REMARK 3 T33: 0.0724 T12: 0.0129
REMARK 3 T13: -0.0077 T23: 0.0200
REMARK 3 L TENSOR
REMARK 3 L11: 0.8395 L22: 1.6963
REMARK 3 L33: 0.3971 L12: -0.0351
REMARK 3 L13: -0.2112 L23: 0.6539
REMARK 3 S TENSOR
REMARK 3 S11: 0.0198 S12: 0.0605 S13: 0.0686
REMARK 3 S21: -0.0529 S22: -0.0396 S23: 0.0175
REMARK 3 S31: -0.0274 S32: -0.0698 S33: 0.0171
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 147 )
REMARK 3 ORIGIN FOR THE GROUP (A): 6.9312 -9.3071 -2.7150
REMARK 3 T TENSOR
REMARK 3 T11: 0.0628 T22: 0.0414
REMARK 3 T33: 0.0813 T12: -0.0240
REMARK 3 T13: 0.0318 T23: 0.0278
REMARK 3 L TENSOR
REMARK 3 L11: 2.7463 L22: 1.4902
REMARK 3 L33: 3.1043 L12: -0.4492
REMARK 3 L13: 0.9792 L23: 0.5113
REMARK 3 S TENSOR
REMARK 3 S11: 0.1206 S12: 0.0022 S13: -0.1203
REMARK 3 S21: 0.0826 S22: 0.0468 S23: -0.1267
REMARK 3 S31: 0.1951 S32: 0.2519 S33: -0.1739
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 148 THROUGH 170 )
REMARK 3 ORIGIN FOR THE GROUP (A): 0.1121 -5.6703 14.8149
REMARK 3 T TENSOR
REMARK 3 T11: 0.1517 T22: 0.1473
REMARK 3 T33: 0.0838 T12: -0.0312
REMARK 3 T13: -0.0099 T23: 0.0151
REMARK 3 L TENSOR
REMARK 3 L11: 1.1380 L22: 5.6097
REMARK 3 L33: 8.1630 L12: -2.5239
REMARK 3 L13: -2.8925 L23: 6.3697
REMARK 3 S TENSOR
REMARK 3 S11: 0.0165 S12: -0.0946 S13: -0.0437
REMARK 3 S21: 0.3719 S22: -0.0414 S23: -0.0055
REMARK 3 S31: 0.3296 S32: -0.1119 S33: 0.0349
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 171 THROUGH 249 )
REMARK 3 ORIGIN FOR THE GROUP (A): -5.8047 4.0206 10.0194
REMARK 3 T TENSOR
REMARK 3 T11: 0.0911 T22: 0.1132
REMARK 3 T33: 0.0647 T12: 0.0028
REMARK 3 T13: -0.0030 T23: 0.0025
REMARK 3 L TENSOR
REMARK 3 L11: 0.9702 L22: 1.7060
REMARK 3 L33: 2.0554 L12: 0.1282
REMARK 3 L13: -0.0381 L23: 0.7698
REMARK 3 S TENSOR
REMARK 3 S11: 0.0389 S12: -0.1181 S13: 0.0543
REMARK 3 S21: 0.1119 S22: -0.1001 S23: 0.1318
REMARK 3 S31: -0.0688 S32: -0.0840 S33: 0.0631
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 250 THROUGH 284 )
REMARK 3 ORIGIN FOR THE GROUP (A): 10.6595 -6.6728 0.2623
REMARK 3 T TENSOR
REMARK 3 T11: 0.0668 T22: 0.0749
REMARK 3 T33: 0.0722 T12: 0.0202
REMARK 3 T13: -0.0180 T23: 0.0310
REMARK 3 L TENSOR
REMARK 3 L11: 2.4733 L22: 2.4018
REMARK 3 L33: 1.8432 L12: 0.4925
REMARK 3 L13: 0.0700 L23: 1.4235
REMARK 3 S TENSOR
REMARK 3 S11: 0.0363 S12: -0.0034 S13: -0.0253
REMARK 3 S21: 0.0375 S22: -0.0004 S23: -0.1099
REMARK 3 S31: 0.0699 S32: 0.0455 S33: -0.0308
REMARK 3 TLS GROUP : 9
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 285 THROUGH 299 )
REMARK 3 ORIGIN FOR THE GROUP (A): -4.4822 -18.1816 -11.0168
REMARK 3 T TENSOR
REMARK 3 T11: 0.1081 T22: 0.1122
REMARK 3 T33: 0.0826 T12: -0.0062
REMARK 3 T13: -0.0127 T23: 0.0030
REMARK 3 L TENSOR
REMARK 3 L11: 7.0761 L22: 3.2903
REMARK 3 L33: 4.2138 L12: 3.6634
REMARK 3 L13: 1.5447 L23: -0.2976
REMARK 3 S TENSOR
REMARK 3 S11: -0.0407 S12: -0.0253 S13: -0.0484
REMARK 3 S21: -0.0732 S22: 0.1401 S23: -0.2782
REMARK 3 S31: 0.2348 S32: -0.1102 S33: -0.0764
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 6DUI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-18.
REMARK 100 THE DEPOSITION ID IS D_1000235251.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-MAR-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37740
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550
REMARK 200 RESOLUTION RANGE LOW (A) : 42.585
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4
REMARK 200 DATA REDUNDANCY : 3.952
REMARK 200 R MERGE (I) : 0.07700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4
REMARK 200 DATA REDUNDANCY IN SHELL : 3.99
REMARK 200 R MERGE FOR SHELL (I) : 0.50700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.690
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 5UPG
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.61
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES HCL, PH 7.5, 50MM CACL2,
REMARK 280 4% (W/V) PROPANOL, 25% (W/V) PEG 3350,
REMARK 280 PSAEA.00166.A.DG15.PD00442 AT 5MG/ML + 1MM ZNCL2 + 1MM BSI
REMARK 280 108451, CRYO = 20%EG: TRAY 298107E10, VAPOR DIFFUSION, SITTING
REMARK 280 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 LYS A 183 CG CD CE NZ
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 OD1 ASP A 161 O HOH A 501 2.01
REMARK 500 OH TYR A 230 O HOH A 502 2.02
REMARK 500 OD1 ASN A 220 O HOH A 503 2.12
REMARK 500 O HOH A 832 O HOH A 841 2.19
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 558 O HOH A 833 1554 2.17
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 THR A 60 33.72 -140.60
REMARK 500 THR A 61 -74.43 -63.53
REMARK 500 SER A 63 171.33 173.99
REMARK 500 MET A 103 -129.15 59.69
REMARK 500 ASP A 159 81.15 -153.92
REMARK 500 SER A 178 -150.41 -109.92
REMARK 500 SER A 178 -151.24 -108.88
REMARK 500 THR A 179 52.42 -104.54
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 92.9
REMARK 620 3 ASP A 241 OD1 146.8 91.5
REMARK 620 4 ASP A 241 OD2 93.9 101.2 53.0
REMARK 620 5 HAY A 401 O29 95.6 166.5 87.1 88.7
REMARK 620 6 HAY A 401 O27 131.8 89.2 81.1 132.8 77.3
REMARK 620 7 J1M A 402 O29 96.6 159.7 90.3 96.0 7.5 71.1
REMARK 620 8 J1M A 402 O27 117.5 88.1 95.5 146.9 78.7 14.4 71.6
REMARK 620 N 1 2 3 4 5 6 7
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue HAY A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue J1M 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 CL A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6CAX RELATED DB: PDB
REMARK 900 RELATED ID: 6C9C RELATED DB: PDB
REMARK 900 RELATED ID: 5UPG RELATED DB: PDB
REMARK 900 RELATED ID: 5VWM RELATED DB: PDB
DBREF 6DUI A 1 303 UNP B7UZI4 LPXC_PSEA8 1 303
SEQADV 6DUI SER A 0 UNP B7UZI4 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 HAY A 401 33
HET J1M A 402 33
HET ZN A 403 1
HET CL A 404 1
HET EDO A 405 4
HET EDO A 406 4
HETNAM HAY (2R)-4-{4-[4-(BENZYLOXY)PHENYL]-2-OXOPYRIDIN-1(2H)-YL}-
HETNAM 2 HAY N-HYDROXY-2-METHYL-2-(METHYLSULFONYL)BUTANAMIDE
HETNAM J1M (2S)-4-{4-[4-(BENZYLOXY)PHENYL]-2-OXOPYRIDIN-1(2H)-YL}-
HETNAM 2 J1M N-HYDROXY-2-METHYL-2-(METHYLSULFONYL)BUTANAMIDE
HETNAM ZN ZINC ION
HETNAM CL CHLORIDE ION
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 HAY C24 H26 N2 O6 S
FORMUL 3 J1M C24 H26 N2 O6 S
FORMUL 4 ZN ZN 2+
FORMUL 5 CL CL 1-
FORMUL 6 EDO 2(C2 H6 O2)
FORMUL 8 HOH *411(H2 O)
HELIX 1 AA1 ARG A 53 VAL A 57 5 5
HELIX 2 AA2 VAL A 76 LEU A 86 1 11
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 2 LEU A 66 LYS A 68 0
SHEET 2 AA3 2 VAL A 71 VAL A 73 -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 GLU A 256 N VAL A 147
SHEET 4 AA4 5 PHE A 152 GLU A 157 1 N SER A 155 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 GLU A 256 N VAL A 147
SHEET 4 AA5 5 PHE A 128 ILE A 131 1 N ILE A 129 O ILE A 254
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 2.09
LINK NE2 HIS A 237 ZN ZN A 403 1555 1555 2.06
LINK OD1 ASP A 241 ZN ZN A 403 1555 1555 2.70
LINK OD2 ASP A 241 ZN ZN A 403 1555 1555 2.08
LINK O29AHAY A 401 ZN ZN A 403 1555 1555 2.11
LINK O27AHAY A 401 ZN ZN A 403 1555 1555 2.08
LINK O29BJ1M A 402 ZN ZN A 403 1555 1555 2.28
LINK O27BJ1M A 402 ZN ZN A 403 1555 1555 2.22
CISPEP 1 ASP A 45 PRO A 46 0 -1.66
SITE 1 AC1 20 LEU A 18 HIS A 19 MET A 62 GLU A 77
SITE 2 AC1 20 HIS A 78 THR A 190 PHE A 191 GLY A 192
SITE 3 AC1 20 PHE A 193 MET A 194 VAL A 216 HIS A 237
SITE 4 AC1 20 LYS A 238 ASP A 241 HIS A 264 J1M A 402
SITE 5 AC1 20 ZN A 403 HOH A 570 HOH A 628 HOH A 675
SITE 1 AC2 17 MET A 62 SER A 63 GLU A 77 HIS A 78
SITE 2 AC2 17 THR A 190 PHE A 191 GLY A 192 MET A 194
SITE 3 AC2 17 ARG A 201 GLY A 209 HIS A 237 ASP A 241
SITE 4 AC2 17 HIS A 264 HAY A 401 ZN A 403 HOH A 504
SITE 5 AC2 17 HOH A 570
SITE 1 AC3 5 HIS A 78 HIS A 237 ASP A 241 HAY A 401
SITE 2 AC3 5 J1M A 402
SITE 1 AC4 2 GLY A 263 LEU A 266
SITE 1 AC5 4 TYR A 230 GLU A 231 ASP A 232 LYS A 236
SITE 1 AC6 6 MET A 1 GLU A 225 THR A 285 GLU A 287
SITE 2 AC6 6 HOH A 554 HOH A 556
CRYST1 35.710 48.000 48.130 111.32 108.56 98.83 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 0.028003 0.004351 0.012609 0.00000
SCALE2 0.000000 0.021083 0.010340 0.00000
SCALE3 0.000000 0.000000 0.024411 0.00000