HEADER OXIDOREDUCTASE 15-NOV-10 3PLN TITLE CRYSTAL STRUCTURE OF KLEBSIELLA PNEUMONIAE UDP-GLUCOSE 6-DEHYDROGENASE TITLE 2 COMPLEXED WITH UDP-GLUCOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-GLUCOSE 6-DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.22; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 484021; SOURCE 4 STRAIN: NTUH-K2044; SOURCE 5 GENE: KP1_3701, UGD; 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: PET28A KEYWDS ROSSMANN FOLD, DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.-Y.CHEN,T.-P.KO,C.-H.LIN,W.-H.CHEN,A.H.-J.WANG REVDAT 3 01-NOV-23 3PLN 1 REMARK SEQADV REVDAT 2 08-NOV-17 3PLN 1 REMARK REVDAT 1 28-SEP-11 3PLN 0 JRNL AUTH Y.Y.CHEN,T.P.KO,C.H.LIN,W.H.CHEN,A.H.WANG JRNL TITL CONFORMATIONAL CHANGE UPON PRODUCT BINDING TO KLEBSIELLA JRNL TITL 2 PNEUMONIAE UDP-GLUCOSE DEHYDROGENASE: A POSSIBLE INHIBITION JRNL TITL 3 MECHANISM FOR THE KEY ENZYME IN POLYMYXIN RESISTANCE. JRNL REF J.STRUCT.BIOL. V. 175 300 2011 JRNL REFN ISSN 1047-8477 JRNL PMID 21536136 JRNL DOI 10.1016/J.JSB.2011.04.010 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 70228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3776 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.12 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2355 REMARK 3 BIN FREE R VALUE : 0.2567 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 361 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 664 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 1.804 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PLN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77013 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 3PID REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL BUFFER (PH 8.0), 0.8M REMARK 280 SODIUM FORMATE, 19-25 % (W/V) PEG 2000 MONOMETHYL ETHER, 2MM UPG REMARK 280 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 53.47000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.60850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.47000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.60850 REMARK 290 SMTRY3 4 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: 5240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 74.63244 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 72.25829 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 A1000 LIES ON A SPECIAL POSITION. 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 MET A 964 REMARK 465 GLY A 965 REMARK 465 SER A 966 REMARK 465 SER A 967 REMARK 465 HIS A 968 REMARK 465 HIS A 969 REMARK 465 HIS A 970 REMARK 465 HIS A 971 REMARK 465 HIS A 972 REMARK 465 HIS A 973 REMARK 465 SER A 974 REMARK 465 SER A 975 REMARK 465 GLY A 976 REMARK 465 LEU A 977 REMARK 465 VAL A 978 REMARK 465 PRO A 979 REMARK 465 ARG A 980 REMARK 465 GLY A 981 REMARK 465 SER A 982 REMARK 465 HIS A 983 REMARK 465 MET A 984 REMARK 465 ALA A 985 REMARK 465 SER A 986 REMARK 465 MET A 987 REMARK 465 THR A 988 REMARK 465 GLY A 989 REMARK 465 GLY A 990 REMARK 465 GLN A 991 REMARK 465 GLN A 992 REMARK 465 MET A 993 REMARK 465 GLY A 994 REMARK 465 ARG A 995 REMARK 465 ILE A 305 REMARK 465 MET A 306 REMARK 465 LYS A 307 REMARK 465 SER A 308 REMARK 465 GLY A 309 REMARK 465 SER A 310 REMARK 465 ASP A 311 REMARK 465 ASN A 312 REMARK 465 PHE A 313 REMARK 465 ARG A 314 REMARK 465 ALA A 315 REMARK 465 ASN A 387 REMARK 465 ASP A 388 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 NE2 GLN A 221 O HOH A 519 2.03 REMARK 500 CE2 TYR A 242 O HOH A 518 2.07 REMARK 500 O HOH A 589 O HOH A 1379 2.07 REMARK 500 O HOH A 454 O HOH A 1089 2.07 REMARK 500 O HOH A 482 O HOH A 1373 2.10 REMARK 500 O HOH A 1060 O HOH A 1358 2.10 REMARK 500 O HOH A 475 O HOH A 517 2.11 REMARK 500 O HOH A 462 O HOH A 536 2.11 REMARK 500 O HOH A 446 O HOH A 1029 2.12 REMARK 500 O HOH A 651 O HOH A 652 2.13 REMARK 500 O HOH A 1080 O HOH A 1381 2.13 REMARK 500 O HOH A 527 O HOH A 566 2.13 REMARK 500 O HOH A 483 O HOH A 663 2.15 REMARK 500 O HOH A 1364 O HOH A 1368 2.16 REMARK 500 O HOH A 437 O HOH A 1243 2.17 REMARK 500 O HOH A 456 O HOH A 1365 2.17 REMARK 500 O HOH A 590 O HOH A 592 2.17 REMARK 500 O HOH A 515 O HOH A 1127 2.17 REMARK 500 O HOH A 457 O HOH A 1368 2.18 REMARK 500 O HOH A 622 O HOH A 623 2.18 REMARK 500 ND2 ASN A 240 O HOH A 660 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 1051 O HOH A 1080 4647 1.94 REMARK 500 O HOH A 1271 O HOH A 1273 2656 2.07 REMARK 500 O HOH A 1161 O HOH A 1236 2656 2.17 REMARK 500 O HOH A 475 O HOH A 649 3545 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 129 CB GLU A 129 CG -0.127 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 TYR A 242 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 324 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 348 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 ASP A 47 109.87 -168.14 REMARK 500 ASN A 135 48.22 -94.50 REMARK 500 ARG A 147 38.68 -142.63 REMARK 500 ASN A 243 23.20 -143.27 REMARK 500 ARG A 303 138.99 79.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 203 0.07 SIDE CHAIN 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 U5P A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PLR RELATED DB: PDB DBREF 3PLN A 1 388 UNP C4XAX5 C4XAX5_KLEPN 1 388 SEQADV 3PLN MET A 964 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLY A 965 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN SER A 966 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN SER A 967 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN HIS A 968 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN HIS A 969 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN HIS A 970 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN HIS A 971 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN HIS A 972 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN HIS A 973 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN SER A 974 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN SER A 975 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLY A 976 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN LEU A 977 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN VAL A 978 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN PRO A 979 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN ARG A 980 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLY A 981 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN SER A 982 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN HIS A 983 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN MET A 984 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN ALA A 985 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN SER A 986 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN MET A 987 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN THR A 988 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLY A 989 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLY A 990 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLN A 991 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLN A 992 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN MET A 993 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLY A 994 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN ARG A 995 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLY A 996 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN SER A 997 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN GLU A 998 UNP C4XAX5 EXPRESSION TAG SEQADV 3PLN PHE A 999 UNP C4XAX5 EXPRESSION TAG SEQRES 1 A 424 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 424 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 424 GLY GLN GLN MET GLY ARG GLY SER GLU PHE MET LYS ILE SEQRES 4 A 424 THR ILE SER GLY THR GLY TYR VAL GLY LEU SER ASN GLY SEQRES 5 A 424 VAL LEU ILE ALA GLN ASN HIS GLU VAL VAL ALA LEU ASP SEQRES 6 A 424 ILE VAL GLN ALA LYS VAL ASP MET LEU ASN GLN LYS ILE SEQRES 7 A 424 SER PRO ILE VAL ASP LYS GLU ILE GLN GLU TYR LEU ALA SEQRES 8 A 424 GLU LYS PRO LEU ASN PHE ARG ALA THR THR ASP LYS HIS SEQRES 9 A 424 ASP ALA TYR ARG ASN ALA ASP TYR VAL ILE ILE ALA THR SEQRES 10 A 424 PRO THR ASP TYR ASP PRO LYS THR ASN TYR PHE ASN THR SEQRES 11 A 424 SER THR VAL GLU ALA VAL ILE ARG ASP VAL THR GLU ILE SEQRES 12 A 424 ASN PRO ASN ALA VAL MET ILE ILE LYS SER THR ILE PRO SEQRES 13 A 424 VAL GLY PHE THR ARG ASP ILE LYS GLU ARG LEU GLY ILE SEQRES 14 A 424 ASP ASN VAL ILE PHE SER PRO GLU PHE LEU ARG GLU GLY SEQRES 15 A 424 ARG ALA LEU TYR ASP ASN LEU HIS PRO SER ARG ILE VAL SEQRES 16 A 424 ILE GLY GLU ARG SER ALA ARG ALA GLU ARG PHE ALA ASP SEQRES 17 A 424 LEU LEU LYS GLU GLY ALA ILE LYS GLN ASP ILE PRO THR SEQRES 18 A 424 LEU PHE THR ASP SER THR GLU ALA GLU ALA ILE LYS LEU SEQRES 19 A 424 PHE ALA ASN THR TYR LEU ALA LEU ARG VAL ALA TYR PHE SEQRES 20 A 424 ASN GLU LEU ASP SER TYR ALA GLU SER GLN GLY LEU ASN SEQRES 21 A 424 SER LYS GLN ILE ILE GLU GLY VAL CYS LEU ASP PRO ARG SEQRES 22 A 424 ILE GLY ASN HIS TYR ASN ASN PRO SER PHE GLY TYR GLY SEQRES 23 A 424 GLY TYR CYS LEU PRO LYS ASP THR LYS GLN LEU LEU ALA SEQRES 24 A 424 ASN TYR GLU SER VAL PRO ASN ASN ILE ILE ALA ALA ILE SEQRES 25 A 424 VAL ASP ALA ASN ARG THR ARG LYS ASP PHE ILE ALA ASP SEQRES 26 A 424 SER ILE LEU ALA ARG LYS PRO LYS VAL VAL GLY VAL TYR SEQRES 27 A 424 ARG LEU ILE MET LYS SER GLY SER ASP ASN PHE ARG ALA SEQRES 28 A 424 SER SER ILE GLN GLY ILE MET LYS ARG ILE LYS ALA LYS SEQRES 29 A 424 GLY ILE PRO VAL ILE ILE TYR GLU PRO VAL MET GLN GLU SEQRES 30 A 424 ASP GLU PHE PHE ASN SER ARG VAL VAL ARG ASP LEU ASN SEQRES 31 A 424 ALA PHE LYS GLN GLU ALA ASP VAL ILE ILE SER ASN ARG SEQRES 32 A 424 MET ALA GLU GLU LEU ALA ASP VAL ALA ASP LYS VAL TYR SEQRES 33 A 424 THR ARG ASP LEU PHE GLY ASN ASP HET U5P A 901 21 HETNAM U5P URIDINE-5'-MONOPHOSPHATE FORMUL 2 U5P C9 H13 N2 O9 P FORMUL 3 HOH *664(H2 O) HELIX 1 1 GLY A 9 GLN A 21 1 13 HELIX 2 2 VAL A 31 GLN A 40 1 10 HELIX 3 3 ASP A 47 LYS A 57 1 11 HELIX 4 4 ASP A 66 ARG A 72 1 7 HELIX 5 5 THR A 94 ASN A 108 1 15 HELIX 6 6 GLY A 122 GLY A 132 1 11 HELIX 7 7 ARG A 147 HIS A 154 1 8 HELIX 8 8 SER A 164 ALA A 178 1 15 HELIX 9 9 ASP A 189 GLY A 222 1 34 HELIX 10 10 ASN A 224 LEU A 234 1 11 HELIX 11 11 CYS A 253 TYR A 265 1 13 HELIX 12 12 ASN A 271 ALA A 293 1 23 HELIX 13 13 SER A 316 LYS A 328 1 13 HELIX 14 14 ASP A 352 ALA A 360 1 9 HELIX 15 15 ALA A 369 ASP A 377 5 9 SHEET 1 A 6 PHE A 61 THR A 64 0 SHEET 2 A 6 GLU A 24 LEU A 28 1 N ALA A 27 O ARG A 62 SHEET 3 A 6 LYS A 2 SER A 6 1 N ILE A 5 O LEU A 28 SHEET 4 A 6 TYR A 76 ILE A 79 1 O ILE A 78 N THR A 4 SHEET 5 A 6 VAL A 112 ILE A 115 1 O ILE A 114 N ILE A 79 SHEET 6 A 6 VAL A 136 PHE A 138 1 O ILE A 137 N ILE A 115 SHEET 1 B 2 ASP A 84 ASP A 86 0 SHEET 2 B 2 TYR A 91 ASN A 93 -1 O ASN A 93 N ASP A 84 SHEET 1 C 2 ILE A 158 ILE A 160 0 SHEET 2 C 2 THR A 185 PHE A 187 1 O LEU A 186 N ILE A 158 SHEET 1 D 6 GLU A 343 PHE A 344 0 SHEET 2 D 6 SER A 347 VAL A 349 -1 O SER A 347 N PHE A 344 SHEET 3 D 6 VAL A 332 TYR A 335 1 N ILE A 334 O ARG A 348 SHEET 4 D 6 VAL A 299 TYR A 302 1 N VAL A 301 O ILE A 333 SHEET 5 D 6 VAL A 362 ILE A 364 1 O ILE A 364 N GLY A 300 SHEET 6 D 6 VAL A 379 TYR A 380 1 O TYR A 380 N ILE A 363 SITE 1 AC1 17 ARG A 144 VAL A 208 ARG A 237 TYR A 242 SITE 2 AC1 17 ASN A 243 ASN A 244 SER A 246 GLY A 250 SITE 3 AC1 17 ARG A 367 HOH A 423 HOH A 462 HOH A 518 SITE 4 AC1 17 HOH A 538 HOH A1257 HOH A1335 HOH A1339 SITE 5 AC1 17 HOH A1341 CRYST1 106.940 63.217 79.152 90.00 114.09 90.00 C 1 2 1 4 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 0.009351 0.000000 0.004181 0.00000 SCALE2 0.000000 0.015819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013839 0.00000