HEADER TRANSFERASE 29-OCT-21 7VTF TITLE CYTIDINE BOUND STRUCTURE OF PSEUDOURIDINE KINASE (PUKI) FROM TITLE 2 ESCHERICHIA COLI STRAIN B COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOURIDINE KINASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PUTATIVE PYRIMIDINE KINASE; COMPND 5 EC: 2.7.1.83; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PSUK, PSUK_1, PSUK_2, A8C65_16945, BMT91_00230, BON75_04205, SOURCE 5 BVCMSHHP019_05067, BVCMSSINP011_02211, D9H68_16155, D9J11_19520, SOURCE 6 E2127_01880, E2128_04080, E2134_03530, FORC82_1677, G9P50_07470, SOURCE 7 GQE64_02140, GQM28_02110, HVV70_14180, HVX33_21995, HVZ33_08660, SOURCE 8 NCTC11022_02147, NCTC13216_04879, NCTC9706_04998, SOURCE 9 SAMEA3752557_00486, WP4S18E08_16210; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS PSEUDOURIDINE KINASE, PSEUDOURDINE, TRANSFERASE, PFKB FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR S.H.KIM,S.RHEE REVDAT 4 29-NOV-23 7VTF 1 REMARK REVDAT 3 11-MAY-22 7VTF 1 JRNL REVDAT 2 13-APR-22 7VTF 1 JRNL REVDAT 1 06-APR-22 7VTF 0 JRNL AUTH S.H.KIM,M.KIM,D.PARK,S.BYUN,S.RHEE JRNL TITL SUBSTRATE-BINDING LOOP INTERACTIONS WITH PSEUDOURIDINE JRNL TITL 2 TRIGGER CONFORMATIONAL CHANGES THAT PROMOTE CATALYTIC JRNL TITL 3 EFFICIENCY OF PSEUDOURIDINE KINASE PUKI. JRNL REF J.BIOL.CHEM. V. 298 01869 2022 JRNL REFN ESSN 1083-351X JRNL PMID 35346685 JRNL DOI 10.1016/J.JBC.2022.101869 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.958 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 98349 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.026 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 36.9542 - 5.3024 0.96 6736 147 0.1981 0.2584 REMARK 3 2 5.3024 - 4.2106 0.99 6890 139 0.1807 0.2265 REMARK 3 3 4.2106 - 3.6789 0.99 6883 140 0.2179 0.3394 REMARK 3 4 3.6789 - 3.3427 0.99 6923 142 0.2406 0.2551 REMARK 3 5 3.3427 - 3.1033 0.99 6948 152 0.2668 0.2993 REMARK 3 6 3.1033 - 2.9204 0.99 6949 132 0.2954 0.3374 REMARK 3 7 2.9204 - 2.7742 1.00 6957 147 0.3253 0.3454 REMARK 3 8 2.7742 - 2.6535 1.00 6911 145 0.3301 0.3848 REMARK 3 9 2.6535 - 2.5513 1.00 6921 146 0.3682 0.3926 REMARK 3 10 2.5513 - 2.4633 1.00 7024 142 0.3813 0.5302 REMARK 3 11 2.4633 - 2.3863 1.00 6946 144 0.3958 0.4049 REMARK 3 12 2.3863 - 2.3181 0.99 6884 142 0.4093 0.3993 REMARK 3 13 2.3181 - 2.2571 0.94 6585 135 0.4210 0.3784 REMARK 3 14 2.2571 - 2.2020 0.97 6799 140 0.4224 0.4266 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) : 0.413 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.655 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.80 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 : 0.004 9241 REMARK 3 ANGLE : 1.013 12586 REMARK 3 CHIRALITY : 0.037 1464 REMARK 3 PLANARITY : 0.005 1624 REMARK 3 DIHEDRAL : 13.090 3196 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 60.9579 -1.9726 14.6469 REMARK 3 T TENSOR REMARK 3 T11: 0.5011 T22: 0.5553 REMARK 3 T33: 0.8621 T12: 0.0478 REMARK 3 T13: -0.0888 T23: 0.0541 REMARK 3 L TENSOR REMARK 3 L11: 0.2610 L22: 0.0607 REMARK 3 L33: -0.0663 L12: -0.1672 REMARK 3 L13: -0.0318 L23: 0.0212 REMARK 3 S TENSOR REMARK 3 S11: -0.0140 S12: 0.0296 S13: 0.0104 REMARK 3 S21: 0.0361 S22: 0.0311 S23: -0.0061 REMARK 3 S31: -0.0786 S32: 0.0434 S33: -0.0116 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN 'A' REMARK 3 SELECTION : CHAIN 'B' REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: CHAIN 'A' REMARK 3 SELECTION : CHAIN 'C' REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: CHAIN 'A' REMARK 3 SELECTION : CHAIN 'D' REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7VTF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1300025347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-20 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97932 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 99598 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 3KZH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM FORMATE, 20% PEG 3350, REMARK 280 5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -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 0.00000 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 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: 4360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 23 REMARK 465 SER A 24 REMARK 465 THR A 104 REMARK 465 GLY A 105 REMARK 465 TYR A 291 REMARK 465 GLU A 310 REMARK 465 CYS A 311 REMARK 465 LEU A 312 REMARK 465 ASN A 313 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 GLU B 3 REMARK 465 GLU B 23 REMARK 465 SER B 24 REMARK 465 THR B 104 REMARK 465 GLY B 105 REMARK 465 GLU B 310 REMARK 465 CYS B 311 REMARK 465 LEU B 312 REMARK 465 ASN B 313 REMARK 465 MET C 1 REMARK 465 ARG C 2 REMARK 465 GLU C 3 REMARK 465 GLU C 23 REMARK 465 SER C 24 REMARK 465 THR C 104 REMARK 465 GLY C 105 REMARK 465 GLU C 310 REMARK 465 CYS C 311 REMARK 465 LEU C 312 REMARK 465 ASN C 313 REMARK 465 MET D 1 REMARK 465 ARG D 2 REMARK 465 GLU D 3 REMARK 465 GLU D 23 REMARK 465 SER D 24 REMARK 465 ASP D 102 REMARK 465 ASN D 103 REMARK 465 THR D 104 REMARK 465 GLY D 105 REMARK 465 GLU D 106 REMARK 465 GLU D 310 REMARK 465 CYS D 311 REMARK 465 LEU D 312 REMARK 465 ASN D 313 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 4 CG CD CE NZ REMARK 470 GLU A 106 CG CD OE1 OE2 REMARK 470 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 277 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 GLU B 106 CG CD OE1 OE2 REMARK 470 ARG B 202 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 277 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 4 CG CD CE NZ REMARK 470 GLU C 106 CG CD OE1 OE2 REMARK 470 ARG C 202 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 277 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 4 CG CD CE NZ REMARK 470 ARG D 134 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 245 CG CD CE NZ REMARK 470 ARG D 277 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 OD1 ASN D 14 OG SER D 95 2.16 REMARK 500 O THR C 76 OG SER C 79 2.18 REMARK 500 O THR B 76 OG SER B 79 2.18 REMARK 500 OD1 ASN C 14 OG SER C 95 2.18 REMARK 500 O THR D 76 OG SER D 79 2.18 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 LEU A 25 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU C 25 CA - CB - CG ANGL. DEV. = 23.0 DEGREES REMARK 500 LEU D 25 CA - CB - CG ANGL. DEV. = 20.3 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 SER A 30 92.72 -61.58 REMARK 500 VAL A 166 -67.91 69.50 REMARK 500 LEU A 199 69.88 -107.82 REMARK 500 SER B 30 91.43 -65.67 REMARK 500 LEU B 101 -167.87 -111.33 REMARK 500 ASP B 102 -168.83 -164.97 REMARK 500 VAL B 166 -67.71 69.47 REMARK 500 LEU B 199 73.05 -109.07 REMARK 500 GLU B 290 -33.66 -33.77 REMARK 500 SER C 30 92.75 -68.15 REMARK 500 LEU C 101 -168.00 -109.35 REMARK 500 VAL C 166 -67.92 69.42 REMARK 500 LEU C 199 69.66 -108.30 REMARK 500 SER D 30 91.80 -65.90 REMARK 500 VAL D 166 -68.18 69.03 REMARK 500 LEU D 199 71.49 -108.83 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 ASN A 26 TYR A 27 -129.56 REMARK 500 ASN C 26 TYR C 27 -138.40 REMARK 500 ASN D 26 TYR D 27 -134.92 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7VTF A 1 313 UNP A0A1V3W5E1_ECOLX DBREF2 7VTF A A0A1V3W5E1 1 313 DBREF1 7VTF B 1 313 UNP A0A1V3W5E1_ECOLX DBREF2 7VTF B A0A1V3W5E1 1 313 DBREF1 7VTF C 1 313 UNP A0A1V3W5E1_ECOLX DBREF2 7VTF C A0A1V3W5E1 1 313 DBREF1 7VTF D 1 313 UNP A0A1V3W5E1_ECOLX DBREF2 7VTF D A0A1V3W5E1 1 313 SEQRES 1 A 313 MET ARG GLU LYS ASP TYR VAL VAL ILE ILE GLY SER ALA SEQRES 2 A 313 ASN ILE ASP VAL ALA GLY TYR SER HIS GLU SER LEU ASN SEQRES 3 A 313 TYR ALA ASP SER ASN PRO GLY LYS ILE LYS PHE THR PRO SEQRES 4 A 313 GLY GLY VAL GLY ARG ASN ILE ALA GLN ASN LEU ALA LEU SEQRES 5 A 313 LEU GLY ASN LYS ALA TRP LEU LEU SER ALA VAL GLY SER SEQRES 6 A 313 ASP PHE TYR GLY GLN SER LEU LEU THR GLN THR ASN GLN SEQRES 7 A 313 SER GLY VAL TYR VAL ASP LYS CYS LEU ILE VAL PRO GLY SEQRES 8 A 313 GLU ASN THR SER SER TYR LEU SER LEU LEU ASP ASN THR SEQRES 9 A 313 GLY GLU MET LEU VAL ALA ILE ASN ASP MET ASN ILE SER SEQRES 10 A 313 ASN ALA ILE THR ALA GLU TYR LEU ALA GLN HIS ARG GLU SEQRES 11 A 313 PHE ILE GLN ARG ALA LYS VAL ILE VAL ALA ASP CYS ASN SEQRES 12 A 313 ILE SER GLU GLU ALA LEU ALA TRP ILE LEU ASP ASN ALA SEQRES 13 A 313 ALA ASN VAL PRO VAL PHE VAL ASP PRO VAL SER ALA TRP SEQRES 14 A 313 LYS CYS VAL LYS VAL ARG ASP ARG LEU ASN GLN ILE HIS SEQRES 15 A 313 THR LEU LYS PRO ASN ARG LEU GLU ALA GLU THR LEU SER SEQRES 16 A 313 GLY ILE ALA LEU SER GLY ARG ASP ASP VAL ALA LYS VAL SEQRES 17 A 313 ALA ALA TRP PHE HIS GLN HIS GLY LEU ASN ARG LEU VAL SEQRES 18 A 313 LEU SER MET GLY GLY ASP GLY VAL TYR TYR SER ASP ILE SEQRES 19 A 313 ARG GLY GLU ASN GLY TRP SER ALA PRO ILE LYS THR ASN SEQRES 20 A 313 VAL ILE ASN VAL THR GLY ALA GLY ASP ALA MET MET ALA SEQRES 21 A 313 GLY LEU ALA SER CYS TRP VAL ASP GLY MET PRO PHE ALA SEQRES 22 A 313 GLU SER VAL ARG PHE ALA GLN GLY CYS SER SER MET ALA SEQRES 23 A 313 LEU SER CYS GLU TYR THR ASN ASN PRO ASP LEU SER ILE SEQRES 24 A 313 ALA ASN VAL ILE SER LEU VAL GLU ASN ALA GLU CYS LEU SEQRES 25 A 313 ASN SEQRES 1 B 313 MET ARG GLU LYS ASP TYR VAL VAL ILE ILE GLY SER ALA SEQRES 2 B 313 ASN ILE ASP VAL ALA GLY TYR SER HIS GLU SER LEU ASN SEQRES 3 B 313 TYR ALA ASP SER ASN PRO GLY LYS ILE LYS PHE THR PRO SEQRES 4 B 313 GLY GLY VAL GLY ARG ASN ILE ALA GLN ASN LEU ALA LEU SEQRES 5 B 313 LEU GLY ASN LYS ALA TRP LEU LEU SER ALA VAL GLY SER SEQRES 6 B 313 ASP PHE TYR GLY GLN SER LEU LEU THR GLN THR ASN GLN SEQRES 7 B 313 SER GLY VAL TYR VAL ASP LYS CYS LEU ILE VAL PRO GLY SEQRES 8 B 313 GLU ASN THR SER SER TYR LEU SER LEU LEU ASP ASN THR SEQRES 9 B 313 GLY GLU MET LEU VAL ALA ILE ASN ASP MET ASN ILE SER SEQRES 10 B 313 ASN ALA ILE THR ALA GLU TYR LEU ALA GLN HIS ARG GLU SEQRES 11 B 313 PHE ILE GLN ARG ALA LYS VAL ILE VAL ALA ASP CYS ASN SEQRES 12 B 313 ILE SER GLU GLU ALA LEU ALA TRP ILE LEU ASP ASN ALA SEQRES 13 B 313 ALA ASN VAL PRO VAL PHE VAL ASP PRO VAL SER ALA TRP SEQRES 14 B 313 LYS CYS VAL LYS VAL ARG ASP ARG LEU ASN GLN ILE HIS SEQRES 15 B 313 THR LEU LYS PRO ASN ARG LEU GLU ALA GLU THR LEU SER SEQRES 16 B 313 GLY ILE ALA LEU SER GLY ARG ASP ASP VAL ALA LYS VAL SEQRES 17 B 313 ALA ALA TRP PHE HIS GLN HIS GLY LEU ASN ARG LEU VAL SEQRES 18 B 313 LEU SER MET GLY GLY ASP GLY VAL TYR TYR SER ASP ILE SEQRES 19 B 313 ARG GLY GLU ASN GLY TRP SER ALA PRO ILE LYS THR ASN SEQRES 20 B 313 VAL ILE ASN VAL THR GLY ALA GLY ASP ALA MET MET ALA SEQRES 21 B 313 GLY LEU ALA SER CYS TRP VAL ASP GLY MET PRO PHE ALA SEQRES 22 B 313 GLU SER VAL ARG PHE ALA GLN GLY CYS SER SER MET ALA SEQRES 23 B 313 LEU SER CYS GLU TYR THR ASN ASN PRO ASP LEU SER ILE SEQRES 24 B 313 ALA ASN VAL ILE SER LEU VAL GLU ASN ALA GLU CYS LEU SEQRES 25 B 313 ASN SEQRES 1 C 313 MET ARG GLU LYS ASP TYR VAL VAL ILE ILE GLY SER ALA SEQRES 2 C 313 ASN ILE ASP VAL ALA GLY TYR SER HIS GLU SER LEU ASN SEQRES 3 C 313 TYR ALA ASP SER ASN PRO GLY LYS ILE LYS PHE THR PRO SEQRES 4 C 313 GLY GLY VAL GLY ARG ASN ILE ALA GLN ASN LEU ALA LEU SEQRES 5 C 313 LEU GLY ASN LYS ALA TRP LEU LEU SER ALA VAL GLY SER SEQRES 6 C 313 ASP PHE TYR GLY GLN SER LEU LEU THR GLN THR ASN GLN SEQRES 7 C 313 SER GLY VAL TYR VAL ASP LYS CYS LEU ILE VAL PRO GLY SEQRES 8 C 313 GLU ASN THR SER SER TYR LEU SER LEU LEU ASP ASN THR SEQRES 9 C 313 GLY GLU MET LEU VAL ALA ILE ASN ASP MET ASN ILE SER SEQRES 10 C 313 ASN ALA ILE THR ALA GLU TYR LEU ALA GLN HIS ARG GLU SEQRES 11 C 313 PHE ILE GLN ARG ALA LYS VAL ILE VAL ALA ASP CYS ASN SEQRES 12 C 313 ILE SER GLU GLU ALA LEU ALA TRP ILE LEU ASP ASN ALA SEQRES 13 C 313 ALA ASN VAL PRO VAL PHE VAL ASP PRO VAL SER ALA TRP SEQRES 14 C 313 LYS CYS VAL LYS VAL ARG ASP ARG LEU ASN GLN ILE HIS SEQRES 15 C 313 THR LEU LYS PRO ASN ARG LEU GLU ALA GLU THR LEU SER SEQRES 16 C 313 GLY ILE ALA LEU SER GLY ARG ASP ASP VAL ALA LYS VAL SEQRES 17 C 313 ALA ALA TRP PHE HIS GLN HIS GLY LEU ASN ARG LEU VAL SEQRES 18 C 313 LEU SER MET GLY GLY ASP GLY VAL TYR TYR SER ASP ILE SEQRES 19 C 313 ARG GLY GLU ASN GLY TRP SER ALA PRO ILE LYS THR ASN SEQRES 20 C 313 VAL ILE ASN VAL THR GLY ALA GLY ASP ALA MET MET ALA SEQRES 21 C 313 GLY LEU ALA SER CYS TRP VAL ASP GLY MET PRO PHE ALA SEQRES 22 C 313 GLU SER VAL ARG PHE ALA GLN GLY CYS SER SER MET ALA SEQRES 23 C 313 LEU SER CYS GLU TYR THR ASN ASN PRO ASP LEU SER ILE SEQRES 24 C 313 ALA ASN VAL ILE SER LEU VAL GLU ASN ALA GLU CYS LEU SEQRES 25 C 313 ASN SEQRES 1 D 313 MET ARG GLU LYS ASP TYR VAL VAL ILE ILE GLY SER ALA SEQRES 2 D 313 ASN ILE ASP VAL ALA GLY TYR SER HIS GLU SER LEU ASN SEQRES 3 D 313 TYR ALA ASP SER ASN PRO GLY LYS ILE LYS PHE THR PRO SEQRES 4 D 313 GLY GLY VAL GLY ARG ASN ILE ALA GLN ASN LEU ALA LEU SEQRES 5 D 313 LEU GLY ASN LYS ALA TRP LEU LEU SER ALA VAL GLY SER SEQRES 6 D 313 ASP PHE TYR GLY GLN SER LEU LEU THR GLN THR ASN GLN SEQRES 7 D 313 SER GLY VAL TYR VAL ASP LYS CYS LEU ILE VAL PRO GLY SEQRES 8 D 313 GLU ASN THR SER SER TYR LEU SER LEU LEU ASP ASN THR SEQRES 9 D 313 GLY GLU MET LEU VAL ALA ILE ASN ASP MET ASN ILE SER SEQRES 10 D 313 ASN ALA ILE THR ALA GLU TYR LEU ALA GLN HIS ARG GLU SEQRES 11 D 313 PHE ILE GLN ARG ALA LYS VAL ILE VAL ALA ASP CYS ASN SEQRES 12 D 313 ILE SER GLU GLU ALA LEU ALA TRP ILE LEU ASP ASN ALA SEQRES 13 D 313 ALA ASN VAL PRO VAL PHE VAL ASP PRO VAL SER ALA TRP SEQRES 14 D 313 LYS CYS VAL LYS VAL ARG ASP ARG LEU ASN GLN ILE HIS SEQRES 15 D 313 THR LEU LYS PRO ASN ARG LEU GLU ALA GLU THR LEU SER SEQRES 16 D 313 GLY ILE ALA LEU SER GLY ARG ASP ASP VAL ALA LYS VAL SEQRES 17 D 313 ALA ALA TRP PHE HIS GLN HIS GLY LEU ASN ARG LEU VAL SEQRES 18 D 313 LEU SER MET GLY GLY ASP GLY VAL TYR TYR SER ASP ILE SEQRES 19 D 313 ARG GLY GLU ASN GLY TRP SER ALA PRO ILE LYS THR ASN SEQRES 20 D 313 VAL ILE ASN VAL THR GLY ALA GLY ASP ALA MET MET ALA SEQRES 21 D 313 GLY LEU ALA SER CYS TRP VAL ASP GLY MET PRO PHE ALA SEQRES 22 D 313 GLU SER VAL ARG PHE ALA GLN GLY CYS SER SER MET ALA SEQRES 23 D 313 LEU SER CYS GLU TYR THR ASN ASN PRO ASP LEU SER ILE SEQRES 24 D 313 ALA ASN VAL ILE SER LEU VAL GLU ASN ALA GLU CYS LEU SEQRES 25 D 313 ASN HET CTN A 401 17 HET CTN B 401 17 HET CTN C 401 17 HET CTN D 401 17 HETNAM CTN 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE HETSYN CTN CYTIDINE FORMUL 5 CTN 4(C9 H13 N3 O5) FORMUL 9 HOH *32(H2 O) HELIX 1 AA1 GLY A 41 GLY A 54 1 14 HELIX 2 AA2 ASP A 66 GLN A 78 1 13 HELIX 3 AA3 MET A 114 ILE A 120 5 7 HELIX 4 AA4 THR A 121 GLN A 127 1 7 HELIX 5 AA5 HIS A 128 ARG A 134 1 7 HELIX 6 AA6 SER A 145 ASN A 155 1 11 HELIX 7 AA7 LYS A 170 ILE A 181 5 12 HELIX 8 AA8 ASN A 187 GLY A 196 1 10 HELIX 9 AA9 ASP A 204 HIS A 215 1 12 HELIX 10 AB1 GLY A 253 ASP A 268 1 16 HELIX 11 AB2 PRO A 271 SER A 288 1 18 HELIX 12 AB3 SER A 298 ASN A 308 1 11 HELIX 13 AB4 GLY B 41 LEU B 53 1 13 HELIX 14 AB5 ASP B 66 GLN B 78 1 13 HELIX 15 AB6 MET B 114 ILE B 120 5 7 HELIX 16 AB7 THR B 121 GLN B 127 1 7 HELIX 17 AB8 HIS B 128 ARG B 134 1 7 HELIX 18 AB9 SER B 145 ASN B 155 1 11 HELIX 19 AC1 LYS B 170 ILE B 181 5 12 HELIX 20 AC2 ASN B 187 GLY B 196 1 10 HELIX 21 AC3 ASP B 204 HIS B 215 1 12 HELIX 22 AC4 GLY B 253 ASP B 268 1 16 HELIX 23 AC5 PRO B 271 SER B 288 1 18 HELIX 24 AC6 SER B 298 ASN B 308 1 11 HELIX 25 AC7 GLY C 41 LEU C 53 1 13 HELIX 26 AC8 ASP C 66 GLN C 78 1 13 HELIX 27 AC9 MET C 114 ILE C 120 5 7 HELIX 28 AD1 THR C 121 GLN C 127 1 7 HELIX 29 AD2 HIS C 128 ARG C 134 1 7 HELIX 30 AD3 SER C 145 ASN C 155 1 11 HELIX 31 AD4 LYS C 170 ILE C 181 5 12 HELIX 32 AD5 ASN C 187 GLY C 196 1 10 HELIX 33 AD6 ASP C 204 HIS C 215 1 12 HELIX 34 AD7 GLY C 253 ASP C 268 1 16 HELIX 35 AD8 PRO C 271 SER C 288 1 18 HELIX 36 AD9 SER C 298 ASN C 308 1 11 HELIX 37 AE1 GLY D 41 GLY D 54 1 14 HELIX 38 AE2 ASP D 66 GLN D 78 1 13 HELIX 39 AE3 MET D 114 ILE D 120 5 7 HELIX 40 AE4 THR D 121 GLN D 127 1 7 HELIX 41 AE5 HIS D 128 ARG D 134 1 7 HELIX 42 AE6 SER D 145 ASN D 155 1 11 HELIX 43 AE7 LYS D 170 ILE D 181 5 12 HELIX 44 AE8 ASN D 187 GLY D 196 1 10 HELIX 45 AE9 ASP D 204 HIS D 215 1 12 HELIX 46 AF1 GLY D 225 ASP D 227 5 3 HELIX 47 AF2 GLY D 253 ASP D 268 1 16 HELIX 48 AF3 PRO D 271 SER D 288 1 18 HELIX 49 AF4 SER D 298 ASN D 308 1 11 SHEET 1 AA1 8 LYS A 56 LEU A 60 0 SHEET 2 AA1 8 TYR A 6 ILE A 10 1 N ILE A 9 O TRP A 58 SHEET 3 AA1 8 VAL A 137 ASP A 141 1 O VAL A 139 N ILE A 10 SHEET 4 AA1 8 VAL A 161 ASP A 164 1 O PHE A 162 N ALA A 140 SHEET 5 AA1 8 THR A 183 LEU A 184 1 O THR A 183 N VAL A 163 SHEET 6 AA1 8 ARG A 219 SER A 223 1 O VAL A 221 N LEU A 184 SHEET 7 AA1 8 VAL A 229 ASP A 233 -1 O TYR A 230 N LEU A 222 SHEET 8 AA1 8 ASN A 238 SER A 241 -1 O SER A 241 N VAL A 229 SHEET 1 AA2 9 ASN A 14 SER A 21 0 SHEET 2 AA2 9 SER A 30 GLY A 40 -1 O THR A 38 N ASP A 16 SHEET 3 AA2 9 VAL B 109 ASP B 113 1 O ASN B 112 N GLY A 33 SHEET 4 AA2 9 SER B 96 LEU B 101 -1 N SER B 96 O ASP B 113 SHEET 5 AA2 9 ASN B 14 SER B 21 1 N GLY B 19 O LEU B 101 SHEET 6 AA2 9 SER B 30 GLY B 40 -1 O GLY B 40 N ASN B 14 SHEET 7 AA2 9 VAL A 109 ASP A 113 1 N ALA A 110 O ASN B 31 SHEET 8 AA2 9 SER A 96 LEU A 101 -1 N LEU A 100 O VAL A 109 SHEET 9 AA2 9 ASN A 14 SER A 21 1 N GLY A 19 O LEU A 101 SHEET 1 AA3 2 ALA A 62 GLY A 64 0 SHEET 2 AA3 2 LEU A 87 VAL A 89 1 O VAL A 89 N VAL A 63 SHEET 1 AA4 8 LYS B 56 LEU B 60 0 SHEET 2 AA4 8 TYR B 6 ILE B 10 1 N ILE B 9 O TRP B 58 SHEET 3 AA4 8 VAL B 137 ASP B 141 1 O VAL B 139 N ILE B 10 SHEET 4 AA4 8 VAL B 161 ASP B 164 1 O PHE B 162 N ALA B 140 SHEET 5 AA4 8 THR B 183 LEU B 184 1 O THR B 183 N VAL B 163 SHEET 6 AA4 8 ARG B 219 SER B 223 1 O VAL B 221 N LEU B 184 SHEET 7 AA4 8 VAL B 229 ASP B 233 -1 O TYR B 230 N LEU B 222 SHEET 8 AA4 8 ASN B 238 SER B 241 -1 O SER B 241 N VAL B 229 SHEET 1 AA5 2 ALA B 62 GLY B 64 0 SHEET 2 AA5 2 LEU B 87 VAL B 89 1 O VAL B 89 N VAL B 63 SHEET 1 AA6 8 LYS C 56 LEU C 60 0 SHEET 2 AA6 8 TYR C 6 ILE C 10 1 N ILE C 9 O TRP C 58 SHEET 3 AA6 8 ILE C 138 ASP C 141 1 O VAL C 139 N ILE C 10 SHEET 4 AA6 8 VAL C 161 ASP C 164 1 O PHE C 162 N ALA C 140 SHEET 5 AA6 8 THR C 183 LEU C 184 1 O THR C 183 N VAL C 163 SHEET 6 AA6 8 ARG C 219 SER C 223 1 O VAL C 221 N LEU C 184 SHEET 7 AA6 8 VAL C 229 ASP C 233 -1 O TYR C 230 N LEU C 222 SHEET 8 AA6 8 ASN C 238 SER C 241 -1 O SER C 241 N VAL C 229 SHEET 1 AA7 9 ASN C 14 SER C 21 0 SHEET 2 AA7 9 SER C 30 GLY C 40 -1 O THR C 38 N ASP C 16 SHEET 3 AA7 9 VAL D 109 ASP D 113 1 O ASN D 112 N GLY C 33 SHEET 4 AA7 9 SER D 96 LEU D 101 -1 N SER D 96 O ASP D 113 SHEET 5 AA7 9 ASN D 14 SER D 21 1 N GLY D 19 O SER D 99 SHEET 6 AA7 9 SER D 30 GLY D 40 -1 O THR D 38 N ASP D 16 SHEET 7 AA7 9 VAL C 109 ASP C 113 1 N ALA C 110 O ASN D 31 SHEET 8 AA7 9 SER C 96 LEU C 101 -1 N SER C 96 O ASP C 113 SHEET 9 AA7 9 ASN C 14 SER C 21 1 N GLY C 19 O SER C 99 SHEET 1 AA8 2 ALA C 62 GLY C 64 0 SHEET 2 AA8 2 LEU C 87 VAL C 89 1 O VAL C 89 N VAL C 63 SHEET 1 AA9 8 LYS D 56 LEU D 60 0 SHEET 2 AA9 8 TYR D 6 ILE D 10 1 N ILE D 9 O TRP D 58 SHEET 3 AA9 8 VAL D 137 ASP D 141 1 O VAL D 139 N ILE D 10 SHEET 4 AA9 8 VAL D 161 ASP D 164 1 O PHE D 162 N ALA D 140 SHEET 5 AA9 8 THR D 183 LEU D 184 1 O THR D 183 N VAL D 163 SHEET 6 AA9 8 ARG D 219 SER D 223 1 O VAL D 221 N LEU D 184 SHEET 7 AA9 8 VAL D 229 ASP D 233 -1 O TYR D 230 N LEU D 222 SHEET 8 AA9 8 ASN D 238 SER D 241 -1 O SER D 241 N VAL D 229 SHEET 1 AB1 2 ALA D 62 GLY D 64 0 SHEET 2 AB1 2 LEU D 87 VAL D 89 1 O VAL D 89 N VAL D 63 CRYST1 185.999 185.999 50.960 90.00 90.00 120.00 P 3 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 0.005376 0.003104 0.000000 0.00000 SCALE2 0.000000 0.006208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019623 0.00000