HEADER HYDROLASE 06-AUG-12 4GGI OBSLTE 08-MAY-13 4GGI 4J6E TITLE STRUCTURE OF LPXI D225A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-2,3-DIACYLGLUCOSAMINE PYROPHOSPHATASE LPXI; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.54; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER CRESCENTUS; SOURCE 3 ORGANISM_TAXID: 565050; SOURCE 4 STRAIN: NA1000 / CB15N; SOURCE 5 GENE: 7330127, CCNA_01987, LPXI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 CENTER FOR STRUCTURES OF MEMBRANE PROTEINS, CSMP, LIPID BINDING, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.E.METZGER IV,J.K.LEE,J.S.FINER-MOORE,C.R.H.RAETZ,R.M.STROUD,CENTER AUTHOR 2 FOR STRUCTURES OF MEMBRANE PROTEINS (CSMP) REVDAT 5 08-MAY-13 4GGI 1 OBSLTE REVDAT 4 17-APR-13 4GGI 1 REMARK REVDAT 3 21-NOV-12 4GGI 1 JRNL REVDAT 2 14-NOV-12 4GGI 1 JRNL REVDAT 1 03-OCT-12 4GGI 0 JRNL AUTH L.E.METZGER,J.K.LEE,J.S.FINER-MOORE,C.R.RAETZ,R.M.STROUD JRNL TITL LPXI STRUCTURES REVEAL HOW A LIPID A PRECURSOR IS JRNL TITL 2 SYNTHESIZED. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1132 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23042606 JRNL DOI 10.1038/NSMB.2393 REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 9603 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 962 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 61.2004 - 4.8199 1.00 1364 152 0.2348 0.2725 REMARK 3 2 4.8199 - 3.8259 1.00 1270 142 0.2086 0.3166 REMARK 3 3 3.8259 - 3.3423 1.00 1246 138 0.2172 0.2856 REMARK 3 4 3.3423 - 3.0367 0.99 1229 137 0.2246 0.2599 REMARK 3 5 3.0367 - 2.8191 0.98 1189 132 0.2482 0.3271 REMARK 3 6 2.8191 - 2.6529 0.96 1191 133 0.2930 0.3521 REMARK 3 7 2.6529 - 2.5200 0.95 1152 128 0.2966 0.3448 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 : 0.83 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 83.58 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.610 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.70830 REMARK 3 B22 (A**2) : 4.70830 REMARK 3 B33 (A**2) : -9.41660 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : -0.00000 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 2073 REMARK 3 ANGLE : 1.525 2802 REMARK 3 CHIRALITY : 0.099 327 REMARK 3 PLANARITY : 0.005 365 REMARK 3 DIHEDRAL : 21.755 786 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (chain A and resid 1:28) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0641 26.0132 -10.4579 REMARK 3 T TENSOR REMARK 3 T11: 1.0998 T22: 1.4714 REMARK 3 T33: 0.6286 T12: 0.3292 REMARK 3 T13: -0.1392 T23: -0.2882 REMARK 3 L TENSOR REMARK 3 L11: 0.8748 L22: 3.3283 REMARK 3 L33: 1.5903 L12: -0.7401 REMARK 3 L13: -1.1774 L23: 1.1161 REMARK 3 S TENSOR REMARK 3 S11: 0.1252 S12: 1.8980 S13: -0.4752 REMARK 3 S21: -1.7726 S22: -0.4505 S23: -0.0305 REMARK 3 S31: 0.6904 S32: 0.6024 S33: 0.2775 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (chain A and resid 29:43) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9343 22.1128 -0.5445 REMARK 3 T TENSOR REMARK 3 T11: 0.7797 T22: 0.8990 REMARK 3 T33: 0.9522 T12: 0.0519 REMARK 3 T13: -0.1767 T23: -0.3624 REMARK 3 L TENSOR REMARK 3 L11: 4.9891 L22: 6.0764 REMARK 3 L33: 5.9873 L12: -4.7385 REMARK 3 L13: -3.5317 L23: 1.0100 REMARK 3 S TENSOR REMARK 3 S11: -0.1189 S12: 0.7937 S13: -1.6876 REMARK 3 S21: -0.8907 S22: -0.0288 S23: 1.9201 REMARK 3 S31: 1.6684 S32: -0.2058 S33: 0.1715 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (chain A and resid 44:120) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9441 29.1699 7.1750 REMARK 3 T TENSOR REMARK 3 T11: 0.4298 T22: 1.1325 REMARK 3 T33: 0.7856 T12: 0.1057 REMARK 3 T13: -0.1059 T23: -0.2054 REMARK 3 L TENSOR REMARK 3 L11: 2.7209 L22: 3.3447 REMARK 3 L33: 1.3758 L12: -2.2568 REMARK 3 L13: 0.1253 L23: 0.9030 REMARK 3 S TENSOR REMARK 3 S11: 0.0921 S12: -0.4233 S13: -0.4335 REMARK 3 S21: 0.0388 S22: 0.6279 S23: -1.0161 REMARK 3 S31: 0.3151 S32: 1.1669 S33: -0.6508 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (chain A and resid 121:130) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7202 35.0802 -8.9994 REMARK 3 T TENSOR REMARK 3 T11: 0.7942 T22: 2.2050 REMARK 3 T33: 1.3719 T12: -0.1015 REMARK 3 T13: 0.4363 T23: 0.1866 REMARK 3 L TENSOR REMARK 3 L11: 4.9225 L22: 5.8284 REMARK 3 L33: 4.2040 L12: 1.2181 REMARK 3 L13: -4.3555 L23: 0.3135 REMARK 3 S TENSOR REMARK 3 S11: -0.0998 S12: 1.5381 S13: 0.6564 REMARK 3 S21: -0.8729 S22: -0.4888 S23: -1.2241 REMARK 3 S31: 0.1713 S32: 0.5169 S33: 0.5494 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (chain A and resid 131:276) REMARK 3 ORIGIN FOR THE GROUP (A): -13.8074 51.1955 -7.5699 REMARK 3 T TENSOR REMARK 3 T11: 0.2883 T22: 0.5488 REMARK 3 T33: 0.1630 T12: -0.2881 REMARK 3 T13: 0.0434 T23: 0.0950 REMARK 3 L TENSOR REMARK 3 L11: 2.1798 L22: 2.9029 REMARK 3 L33: 3.1711 L12: 1.5122 REMARK 3 L13: -1.1602 L23: -0.1780 REMARK 3 S TENSOR REMARK 3 S11: -0.3745 S12: 0.2997 S13: -0.2270 REMARK 3 S21: -0.3954 S22: 0.2096 S23: -0.3893 REMARK 3 S31: -0.0607 S32: 0.5381 S33: 0.0911 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 4GGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-12. REMARK 100 THE RCSB ID CODE IS RCSB074153. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-11 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11 REMARK 200 MONOCHROMATOR : DOUBLECRYSTALSI111 REMARK 200 OPTICS : DOUBLECRYSTALSI111 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9603 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.520 REMARK 200 RESOLUTION RANGE LOW (A) : 61.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : 0.12700 REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 7.5-9.0, 180-200 MM REMARK 280 NACL, 1.3-1.6 M (NH4)2SO4, AND 6% V/V GLYCEROL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.09667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.19333 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 40.64500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 67.74167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.54833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.09667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 54.19333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 67.74167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 40.64500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 13.54833 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 TWO FOLD CRYSTALLOGRAPHIC OPERATOR. 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: 2290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 0.500000 0.866025 0.000000 -53.64850 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 92.92193 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 13.54833 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 GLY A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLN A 220 REMARK 465 GLU A 221 REMARK 465 THR A 222 REMARK 465 GLN A 277 REMARK 465 GLU A 278 REMARK 465 ARG A 279 REMARK 465 PRO A 280 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 LYS A 3 CG CD CE NZ REMARK 470 LYS A 91 CG CD CE NZ REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 GLU A 127 CG CD OE1 OE2 REMARK 470 GLU A 199 CG CD OE1 OE2 REMARK 470 ARG A 207 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 257 CG CD NE CZ NH1 NH2 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 OE1 GLU A 121 O HOH A 416 2.10 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 OD1 ASP A 67 NH1 ARG A 34 5554 1.73 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 PRO A 14 -16.62 -45.22 REMARK 500 GLU A 16 17.90 -59.53 REMARK 500 LEU A 17 -38.74 -133.62 REMARK 500 SER A 19 -80.48 -61.83 REMARK 500 HIS A 20 -13.05 -46.36 REMARK 500 ALA A 23 -105.94 -77.24 REMARK 500 ALA A 24 11.60 -47.40 REMARK 500 PHE A 28 163.19 -23.27 REMARK 500 SER A 40 25.15 -59.84 REMARK 500 LEU A 41 -11.13 -161.98 REMARK 500 ASP A 42 161.79 -49.28 REMARK 500 ARG A 43 67.88 -13.64 REMARK 500 PRO A 45 171.84 -55.14 REMARK 500 GLU A 53 67.13 -58.90 REMARK 500 SER A 81 -65.73 -28.06 REMARK 500 LEU A 83 -159.75 -66.72 REMARK 500 ASP A 86 115.82 -162.75 REMARK 500 SER A 95 -3.08 -54.87 REMARK 500 LEU A 96 -67.73 -91.96 REMARK 500 GLU A 116 -35.47 -39.10 REMARK 500 GLU A 118 1.13 -52.19 REMARK 500 GLU A 123 124.31 148.64 REMARK 500 GLU A 131 -89.87 -123.27 REMARK 500 MET A 132 47.80 -100.88 REMARK 500 GLU A 147 6.62 -58.86 REMARK 500 ILE A 167 -83.18 -62.75 REMARK 500 ALA A 183 -105.48 -120.87 REMARK 500 LYS A 217 58.92 71.66 REMARK 500 VAL A 224 -23.98 -141.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 42 ARG A 43 -148.96 REMARK 500 ARG A 43 TYR A 44 139.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG A 26 24.2 L L OUTSIDE RANGE REMARK 500 ARG A 43 20.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDG A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GGM RELATED DB: PDB REMARK 900 WILD-TYPE REMARK 900 RELATED ID: CSMP-167 RELATED DB: TARGETTRACK DBREF 4GGI A 1 280 UNP B8GWR0 B8GWR0_CAUCN 1 280 SEQADV 4GGI GLY A -2 UNP B8GWR0 EXPRESSION TAG SEQADV 4GGI HIS A -1 UNP B8GWR0 EXPRESSION TAG SEQADV 4GGI MET A 0 UNP B8GWR0 EXPRESSION TAG SEQADV 4GGI ALA A 225 UNP B8GWR0 ASP 225 ENGINEERED MUTATION SEQRES 1 A 283 GLY HIS MET MET ARG LYS LEU GLY LEU ILE ALA GLY GLY SEQRES 2 A 283 GLY ALA LEU PRO VAL GLU LEU ALA SER HIS CYS GLU ALA SEQRES 3 A 283 ALA GLY ARG ALA PHE ALA VAL MET ARG LEU ARG SER PHE SEQRES 4 A 283 ALA ASP PRO SER LEU ASP ARG TYR PRO GLY ALA ASP VAL SEQRES 5 A 283 GLY ILE GLY GLU PHE GLY LYS ILE PHE LYS ALA LEU ARG SEQRES 6 A 283 ALA GLU GLY CYS ASP VAL VAL CYS PHE ALA GLY ASN VAL SEQRES 7 A 283 SER ARG PRO ASP PHE SER ALA LEU MET PRO ASP ALA ARG SEQRES 8 A 283 GLY LEU LYS VAL LEU PRO SER LEU ILE VAL ALA ALA ARG SEQRES 9 A 283 LYS GLY ASP ASP ALA LEU LEU ARG ARG VAL LEU ASP GLU SEQRES 10 A 283 PHE GLU LYS GLU GLY PHE GLU ILE GLU GLY ALA HIS GLU SEQRES 11 A 283 VAL MET GLY GLU MET THR LEU PRO ARG GLY ARG LEU GLY SEQRES 12 A 283 LYS VAL SER PRO ALA PRO GLU HIS MET ALA ASP ILE ASP SEQRES 13 A 283 LYS ALA LEU ASP VAL ALA ARG GLU ILE GLY ARG LEU ASP SEQRES 14 A 283 ILE GLY GLN GLY ALA VAL VAL CYS GLU GLY LEU VAL LEU SEQRES 15 A 283 ALA VAL GLU ALA GLN GLU GLY THR ASP ALA MET LEU ARG SEQRES 16 A 283 ARG VAL ALA ASP LEU PRO GLU ALA ILE ARG GLY ARG ALA SEQRES 17 A 283 GLU ARG ARG LEU GLY VAL LEU ALA LYS ALA PRO LYS PRO SEQRES 18 A 283 ILE GLN GLU THR ARG VAL ALA LEU PRO THR ILE GLY VAL SEQRES 19 A 283 ALA THR ILE HIS ARG ALA ALA ARG ALA GLY LEU ALA GLY SEQRES 20 A 283 ILE VAL GLY GLU ALA GLY ARG LEU LEU VAL VAL ASP ARG SEQRES 21 A 283 GLU ALA VAL ILE ALA ALA ALA ASP ASP LEU GLY LEU PHE SEQRES 22 A 283 VAL LEU GLY VAL ASP PRO GLN GLU ARG PRO HET UDG A 301 68 HETNAM UDG (2R,3R,4R,5S,6R)-2-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4- HETNAM 2 UDG DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4- HETNAM 3 UDG DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY) HETNAM 4 UDG PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-5-HYDROXY-6- HETNAM 5 UDG (HYDROXYMETHYL)-3-{[(3R)-3- HETNAM 6 UDG HYDROXYTETRADECANOYL]AMINO}TETRAHYDRO-2H-PYRAN-4-YL HETNAM 7 UDG (3R)-3-HYDROXYTETRADECANOATE FORMUL 2 UDG C43 H77 N3 O20 P2 FORMUL 3 HOH *19(H2 O) HELIX 1 1 SER A 19 ALA A 24 1 6 HELIX 2 2 GLY A 55 GLY A 65 1 11 HELIX 3 3 ASP A 86 LEU A 90 5 5 HELIX 4 4 LEU A 93 GLY A 103 1 11 HELIX 5 5 ASP A 105 GLU A 118 1 14 HELIX 6 6 ALA A 125 THR A 133 1 9 HELIX 7 7 ALA A 145 GLU A 147 5 3 HELIX 8 8 HIS A 148 LEU A 165 1 18 HELIX 9 9 GLY A 186 LEU A 197 1 12 HELIX 10 10 PRO A 198 ARG A 202 5 5 HELIX 11 11 GLY A 230 ALA A 240 1 11 HELIX 12 12 ASP A 256 GLY A 268 1 13 SHEET 1 A 4 GLY A 46 VAL A 49 0 SHEET 2 A 4 VAL A 30 LEU A 33 1 N ARG A 32 O VAL A 49 SHEET 3 A 4 GLY A 5 ALA A 8 1 N LEU A 6 O MET A 31 SHEET 4 A 4 VAL A 69 ALA A 72 1 O CYS A 70 N ILE A 7 SHEET 1 B 6 GLY A 137 ARG A 138 0 SHEET 2 B 6 PHE A 270 VAL A 274 -1 O GLY A 273 N GLY A 137 SHEET 3 B 6 GLY A 244 GLU A 248 1 N GLY A 247 O VAL A 274 SHEET 4 B 6 VAL A 211 LYS A 214 1 N LEU A 212 O VAL A 246 SHEET 5 B 6 GLY A 170 CYS A 174 -1 N ALA A 171 O ALA A 213 SHEET 6 B 6 LEU A 177 VAL A 181 -1 O LEU A 179 N VAL A 172 SHEET 1 C 2 THR A 228 ILE A 229 0 SHEET 2 C 2 LEU A 253 VAL A 254 1 O LEU A 253 N ILE A 229 CISPEP 1 LYS A 3 LEU A 4 0 -4.14 CISPEP 2 ARG A 26 ALA A 27 0 -29.78 CISPEP 3 PRO A 216 LYS A 217 0 26.02 SITE 1 AC1 25 GLY A 10 ALA A 12 LEU A 13 ILE A 51 SITE 2 AC1 25 ILE A 57 PHE A 71 GLY A 73 ASN A 74 SITE 3 AC1 25 VAL A 75 ASP A 104 LEU A 108 VAL A 111 SITE 4 AC1 25 GLN A 169 GLU A 182 THR A 187 ASP A 188 SITE 5 AC1 25 LYS A 214 LEU A 226 THR A 228 ILE A 229 SITE 6 AC1 25 GLY A 230 VAL A 231 ALA A 232 THR A 233 SITE 7 AC1 25 HOH A 417 CRYST1 107.297 107.297 81.290 90.00 90.00 120.00 P 61 2 2 12 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 0.009320 0.005381 0.000000 0.00000 SCALE2 0.000000 0.010762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012302 0.00000