HEADER RNA BINDING PROTEIN/RNA 19-JAN-22 7WNU TITLE MYCOBACTERIUM TUBERCULOSIS RNASE J COMPLEX WITH 7NT RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE J; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNASE J,BETA-LACTAMASE,PENICILLINASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3'); COMPND 9 CHAIN: C, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RNJ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,J.HU,L.BAO,B.ZHAN,Z.LI REVDAT 3 04-SEP-24 7WNU 1 JRNL REVDAT 2 29-NOV-23 7WNU 1 REMARK REVDAT 1 25-JAN-23 7WNU 0 JRNL AUTH L.BAO,J.HU,B.ZHAN,M.CHI,Z.LI,S.WANG,C.SHAN,Z.ZHAO,Y.GUO, JRNL AUTH 2 X.DING,C.JI,S.TAO,T.NI,X.ZHANG,G.ZHAO,J.LI JRNL TITL STRUCTURAL INSIGHTS INTO RNASE J THAT PLAYS AN ESSENTIAL JRNL TITL 2 ROLE IN MYCOBACTERIUM TUBERCULOSIS RNA METABOLISM JRNL REF NAT COMMUN V. 14 2280 2023 JRNL REFN ESSN 2041-1723 JRNL DOI 10.1038/S41467-023-38045-Z REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21631 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1067 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 42.8800 - 6.3900 0.99 2677 153 0.1774 0.2397 REMARK 3 2 6.3900 - 5.0800 1.00 2590 134 0.1905 0.2174 REMARK 3 3 5.0800 - 4.4400 1.00 2607 111 0.1518 0.1955 REMARK 3 4 4.4400 - 4.0300 1.00 2547 137 0.1647 0.2303 REMARK 3 5 4.0300 - 3.7400 1.00 2519 133 0.1806 0.2317 REMARK 3 6 3.7400 - 3.5200 1.00 2577 131 0.2020 0.2777 REMARK 3 7 3.5200 - 3.3500 1.00 2500 154 0.2234 0.2738 REMARK 3 8 3.3500 - 3.2000 1.00 2547 114 0.2490 0.3322 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) : 0.365 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.949 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.03 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 : 0.011 8721 REMARK 3 ANGLE : 1.343 11928 REMARK 3 CHIRALITY : 0.078 1427 REMARK 3 PLANARITY : 0.012 1514 REMARK 3 DIHEDRAL : 23.001 3230 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7WNU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300027071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21660 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 42.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04050 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.15600 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: 3ZQ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE REMARK 280 0.1 M HEPES PH 7.5 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 96.05000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 96.05000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.03000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.69000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.03000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.69000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 96.05000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.03000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.69000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.05000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.03000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.69000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -163.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 ASP A 2 REMARK 465 VAL A 3 REMARK 465 ASP A 4 REMARK 465 LEU A 5 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 VAL B 3 REMARK 465 ASP B 4 REMARK 465 A D 7 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 ASP A 85 CG OD1 OD2 REMARK 470 ARG A 280 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 324 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 456 CG OD1 OD2 REMARK 470 GLU B 26 CG CD OE1 OE2 REMARK 470 ARG B 280 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 293 CG CD OE1 OE2 REMARK 470 ARG B 324 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 528 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 OG SER A 240 OP1 A C 3 2.05 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 HIS A 66 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 ASP A 170 CB - CA - C ANGL. DEV. = 13.1 DEGREES REMARK 500 ASP A 170 CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 495 CB - CA - C ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG A 495 N - CA - C ANGL. DEV. = 24.8 DEGREES REMARK 500 ARG A 547 N - CA - C ANGL. DEV. = -17.1 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 MET A 31 118.07 -161.58 REMARK 500 ASP A 44 155.63 78.09 REMARK 500 CYS A 45 99.55 -166.60 REMARK 500 MET A 64 23.90 -79.08 REMARK 500 ARG A 70 39.30 -85.18 REMARK 500 HIS A 81 -169.22 -165.46 REMARK 500 ILE A 87 10.17 -140.44 REMARK 500 ALA A 89 30.53 -90.65 REMARK 500 ARG A 97 74.93 -166.71 REMARK 500 ALA A 113 -71.55 -47.75 REMARK 500 PHE A 173 45.35 -108.25 REMARK 500 LEU A 176 56.50 -140.99 REMARK 500 ASP A 298 9.08 -69.12 REMARK 500 SER A 313 -170.41 -66.62 REMARK 500 GLU A 322 43.85 -101.91 REMARK 500 SER A 325 0.73 88.41 REMARK 500 SER A 338 -176.67 -171.02 REMARK 500 GLU A 424 178.84 -57.45 REMARK 500 ALA A 433 74.86 53.57 REMARK 500 LEU A 468 3.26 -63.16 REMARK 500 SER A 494 -55.29 -144.59 REMARK 500 ARG A 495 71.04 52.85 REMARK 500 PHE A 497 -43.41 -131.93 REMARK 500 ASP A 500 97.47 -68.27 REMARK 500 LYS A 502 38.06 -97.86 REMARK 500 MET B 31 118.11 -166.59 REMARK 500 ASP B 44 154.63 64.89 REMARK 500 CYS B 45 76.96 -163.88 REMARK 500 GLU B 68 -56.98 -25.67 REMARK 500 ARG B 97 73.87 -155.08 REMARK 500 PRO B 98 -3.89 -54.68 REMARK 500 HIS B 136 64.89 -150.79 REMARK 500 ASP B 170 95.57 -66.81 REMARK 500 ARG B 181 77.78 -118.99 REMARK 500 ASP B 184 66.67 -102.51 REMARK 500 ALA B 252 -73.14 -64.33 REMARK 500 SER B 260 119.17 -160.74 REMARK 500 ARG B 280 93.67 64.81 REMARK 500 THR B 294 -79.76 -75.66 REMARK 500 THR B 304 -165.34 -119.47 REMARK 500 SER B 319 2.93 -69.97 REMARK 500 SER B 338 -175.06 -171.30 REMARK 500 ALA B 368 -162.62 -129.82 REMARK 500 ARG B 389 66.12 35.94 REMARK 500 HIS B 397 54.78 38.47 REMARK 500 ALA B 423 78.67 -116.56 REMARK 500 ASN B 425 130.71 -30.30 REMARK 500 LEU B 468 1.93 -64.56 REMARK 500 GLN B 485 112.88 -34.92 REMARK 500 LEU B 487 -12.38 67.61 REMARK 500 REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS. 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 GLU B 310 PRO B 311 -148.73 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 ARG A 320 0.29 SIDE CHAIN REMARK 500 ARG B 65 0.18 SIDE CHAIN 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 81 NE2 REMARK 620 2 HIS A 83 NE2 95.6 REMARK 620 3 HIS A 148 NE2 104.0 78.8 REMARK 620 4 ASP A 170 OD2 96.3 151.2 123.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 86 NE2 REMARK 620 2 HIS A 397 NE2 81.6 REMARK 620 3 A C 2 OP2 140.1 126.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 81 NE2 REMARK 620 2 HIS B 83 NE2 96.8 REMARK 620 3 ASP B 170 OD2 90.3 106.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 86 NE2 REMARK 620 2 ASP B 170 OD2 95.8 REMARK 620 3 HIS B 397 NE2 80.8 109.4 REMARK 620 4 A D 2 OP2 145.3 76.6 133.8 REMARK 620 N 1 2 3 DBREF 7WNU A 1 558 UNP P9WGZ9 RNJ_MYCTU 1 558 DBREF 7WNU B 1 558 UNP P9WGZ9 RNJ_MYCTU 1 558 DBREF 7WNU C 1 7 PDB 7WNU 7WNU 1 7 DBREF 7WNU D 1 7 PDB 7WNU 7WNU 1 7 SEQRES 1 A 558 MET ASP VAL ASP LEU PRO PRO PRO GLY PRO LEU THR SER SEQRES 2 A 558 GLY GLY LEU ARG VAL THR ALA LEU GLY GLY ILE ASN GLU SEQRES 3 A 558 ILE GLY ARG ASN MET THR VAL PHE GLU HIS LEU GLY ARG SEQRES 4 A 558 LEU LEU ILE ILE ASP CYS GLY VAL LEU PHE PRO GLY HIS SEQRES 5 A 558 ASP GLU PRO GLY VAL ASP LEU ILE LEU PRO ASP MET ARG SEQRES 6 A 558 HIS VAL GLU ASP ARG LEU ASP ASP ILE GLU ALA LEU VAL SEQRES 7 A 558 LEU THR HIS GLY HIS GLU ASP HIS ILE GLY ALA ILE PRO SEQRES 8 A 558 PHE LEU LEU LYS LEU ARG PRO ASP ILE PRO VAL VAL GLY SEQRES 9 A 558 SER LYS PHE THR LEU ALA LEU VAL ALA GLU LYS CYS ARG SEQRES 10 A 558 GLU TYR ARG ILE THR PRO VAL PHE VAL GLU VAL ARG GLU SEQRES 11 A 558 GLY GLN SER THR ARG HIS GLY VAL PHE GLU CYS GLU TYR SEQRES 12 A 558 PHE ALA VAL ASN HIS SER THR PRO ASP ALA LEU ALA ILE SEQRES 13 A 558 ALA VAL TYR THR GLY ALA GLY THR ILE LEU HIS THR GLY SEQRES 14 A 558 ASP ILE LYS PHE ASP GLN LEU PRO PRO ASP GLY ARG PRO SEQRES 15 A 558 THR ASP LEU PRO GLY MET SER ARG LEU GLY ASP THR GLY SEQRES 16 A 558 VAL ASP LEU LEU LEU CYS ASP SER THR ASN ALA GLU ILE SEQRES 17 A 558 PRO GLY VAL GLY PRO SER GLU SER GLU VAL GLY PRO THR SEQRES 18 A 558 LEU HIS ARG LEU ILE ARG GLY ALA ASP GLY ARG VAL ILE SEQRES 19 A 558 VAL ALA CYS PHE ALA SER ASN VAL ASP ARG VAL GLN GLN SEQRES 20 A 558 ILE ILE ASP ALA ALA VAL ALA LEU GLY ARG ARG VAL SER SEQRES 21 A 558 PHE VAL GLY ARG SER MET VAL ARG ASN MET ARG VAL ALA SEQRES 22 A 558 ARG GLN LEU GLY PHE LEU ARG VAL ALA ASP SER ASP LEU SEQRES 23 A 558 ILE ASP ILE ALA ALA ALA GLU THR MET ALA PRO ASP GLN SEQRES 24 A 558 VAL VAL LEU ILE THR THR GLY THR GLN GLY GLU PRO MET SEQRES 25 A 558 SER ALA LEU SER ARG MET SER ARG GLY GLU HIS ARG SER SEQRES 26 A 558 ILE THR LEU THR ALA GLY ASP LEU ILE VAL LEU SER SER SEQRES 27 A 558 SER LEU ILE PRO GLY ASN GLU GLU ALA VAL PHE GLY VAL SEQRES 28 A 558 ILE ASP ALA LEU SER LYS ILE GLY ALA ARG VAL VAL THR SEQRES 29 A 558 ASN ALA GLN ALA ARG VAL HIS VAL SER GLY HIS ALA TYR SEQRES 30 A 558 ALA GLY GLU LEU LEU PHE LEU TYR ASN GLY VAL ARG PRO SEQRES 31 A 558 ARG ASN VAL MET PRO VAL HIS GLY THR TRP ARG MET LEU SEQRES 32 A 558 ARG ALA ASN ALA LYS LEU ALA ALA SER THR GLY VAL PRO SEQRES 33 A 558 GLN GLU SER ILE LEU LEU ALA GLU ASN GLY VAL SER VAL SEQRES 34 A 558 ASP LEU VAL ALA GLY LYS ALA SER ILE SER GLY ALA VAL SEQRES 35 A 558 PRO VAL GLY LYS MET PHE VAL ASP GLY LEU ILE ALA GLY SEQRES 36 A 558 ASP VAL GLY ASP ILE THR LEU GLY GLU ARG LEU ILE LEU SEQRES 37 A 558 SER SER GLY PHE VAL ALA VAL THR VAL VAL VAL ARG ARG SEQRES 38 A 558 GLY THR GLY GLN PRO LEU ALA ALA PRO HIS LEU HIS SER SEQRES 39 A 558 ARG GLY PHE SER GLU ASP PRO LYS ALA LEU GLU PRO ALA SEQRES 40 A 558 VAL ARG LYS VAL GLU ALA GLU LEU GLU SER LEU VAL ALA SEQRES 41 A 558 ALA ASN VAL THR ASP PRO ILE ARG ILE ALA GLN GLY VAL SEQRES 42 A 558 ARG ARG THR VAL GLY LYS TRP VAL GLY GLU THR TYR ARG SEQRES 43 A 558 ARG GLN PRO MET ILE VAL PRO THR VAL ILE GLU VAL SEQRES 1 B 558 MET ASP VAL ASP LEU PRO PRO PRO GLY PRO LEU THR SER SEQRES 2 B 558 GLY GLY LEU ARG VAL THR ALA LEU GLY GLY ILE ASN GLU SEQRES 3 B 558 ILE GLY ARG ASN MET THR VAL PHE GLU HIS LEU GLY ARG SEQRES 4 B 558 LEU LEU ILE ILE ASP CYS GLY VAL LEU PHE PRO GLY HIS SEQRES 5 B 558 ASP GLU PRO GLY VAL ASP LEU ILE LEU PRO ASP MET ARG SEQRES 6 B 558 HIS VAL GLU ASP ARG LEU ASP ASP ILE GLU ALA LEU VAL SEQRES 7 B 558 LEU THR HIS GLY HIS GLU ASP HIS ILE GLY ALA ILE PRO SEQRES 8 B 558 PHE LEU LEU LYS LEU ARG PRO ASP ILE PRO VAL VAL GLY SEQRES 9 B 558 SER LYS PHE THR LEU ALA LEU VAL ALA GLU LYS CYS ARG SEQRES 10 B 558 GLU TYR ARG ILE THR PRO VAL PHE VAL GLU VAL ARG GLU SEQRES 11 B 558 GLY GLN SER THR ARG HIS GLY VAL PHE GLU CYS GLU TYR SEQRES 12 B 558 PHE ALA VAL ASN HIS SER THR PRO ASP ALA LEU ALA ILE SEQRES 13 B 558 ALA VAL TYR THR GLY ALA GLY THR ILE LEU HIS THR GLY SEQRES 14 B 558 ASP ILE LYS PHE ASP GLN LEU PRO PRO ASP GLY ARG PRO SEQRES 15 B 558 THR ASP LEU PRO GLY MET SER ARG LEU GLY ASP THR GLY SEQRES 16 B 558 VAL ASP LEU LEU LEU CYS ASP SER THR ASN ALA GLU ILE SEQRES 17 B 558 PRO GLY VAL GLY PRO SER GLU SER GLU VAL GLY PRO THR SEQRES 18 B 558 LEU HIS ARG LEU ILE ARG GLY ALA ASP GLY ARG VAL ILE SEQRES 19 B 558 VAL ALA CYS PHE ALA SER ASN VAL ASP ARG VAL GLN GLN SEQRES 20 B 558 ILE ILE ASP ALA ALA VAL ALA LEU GLY ARG ARG VAL SER SEQRES 21 B 558 PHE VAL GLY ARG SER MET VAL ARG ASN MET ARG VAL ALA SEQRES 22 B 558 ARG GLN LEU GLY PHE LEU ARG VAL ALA ASP SER ASP LEU SEQRES 23 B 558 ILE ASP ILE ALA ALA ALA GLU THR MET ALA PRO ASP GLN SEQRES 24 B 558 VAL VAL LEU ILE THR THR GLY THR GLN GLY GLU PRO MET SEQRES 25 B 558 SER ALA LEU SER ARG MET SER ARG GLY GLU HIS ARG SER SEQRES 26 B 558 ILE THR LEU THR ALA GLY ASP LEU ILE VAL LEU SER SER SEQRES 27 B 558 SER LEU ILE PRO GLY ASN GLU GLU ALA VAL PHE GLY VAL SEQRES 28 B 558 ILE ASP ALA LEU SER LYS ILE GLY ALA ARG VAL VAL THR SEQRES 29 B 558 ASN ALA GLN ALA ARG VAL HIS VAL SER GLY HIS ALA TYR SEQRES 30 B 558 ALA GLY GLU LEU LEU PHE LEU TYR ASN GLY VAL ARG PRO SEQRES 31 B 558 ARG ASN VAL MET PRO VAL HIS GLY THR TRP ARG MET LEU SEQRES 32 B 558 ARG ALA ASN ALA LYS LEU ALA ALA SER THR GLY VAL PRO SEQRES 33 B 558 GLN GLU SER ILE LEU LEU ALA GLU ASN GLY VAL SER VAL SEQRES 34 B 558 ASP LEU VAL ALA GLY LYS ALA SER ILE SER GLY ALA VAL SEQRES 35 B 558 PRO VAL GLY LYS MET PHE VAL ASP GLY LEU ILE ALA GLY SEQRES 36 B 558 ASP VAL GLY ASP ILE THR LEU GLY GLU ARG LEU ILE LEU SEQRES 37 B 558 SER SER GLY PHE VAL ALA VAL THR VAL VAL VAL ARG ARG SEQRES 38 B 558 GLY THR GLY GLN PRO LEU ALA ALA PRO HIS LEU HIS SER SEQRES 39 B 558 ARG GLY PHE SER GLU ASP PRO LYS ALA LEU GLU PRO ALA SEQRES 40 B 558 VAL ARG LYS VAL GLU ALA GLU LEU GLU SER LEU VAL ALA SEQRES 41 B 558 ALA ASN VAL THR ASP PRO ILE ARG ILE ALA GLN GLY VAL SEQRES 42 B 558 ARG ARG THR VAL GLY LYS TRP VAL GLY GLU THR TYR ARG SEQRES 43 B 558 ARG GLN PRO MET ILE VAL PRO THR VAL ILE GLU VAL SEQRES 1 C 7 A A A A A A A SEQRES 1 D 7 A A A A A A A HET ZN A 601 1 HET ZN A 602 1 HET ZN B 601 1 HET ZN B 602 1 HETNAM ZN ZINC ION FORMUL 5 ZN 4(ZN 2+) HELIX 1 AA1 ASP A 63 VAL A 67 5 5 HELIX 2 AA2 ARG A 70 ASP A 72 5 3 HELIX 3 AA3 HIS A 83 GLY A 88 1 6 HELIX 4 AA4 ILE A 90 LYS A 95 1 6 HELIX 5 AA5 SER A 105 GLU A 118 1 14 HELIX 6 AA6 ASP A 184 THR A 194 1 11 HELIX 7 AA7 SER A 214 ALA A 229 1 16 HELIX 8 AA8 ASN A 241 LEU A 255 1 15 HELIX 9 AA9 GLY A 263 LEU A 276 1 14 HELIX 10 AB1 ALA A 282 LEU A 286 5 5 HELIX 11 AB2 ASP A 288 MET A 295 1 8 HELIX 12 AB3 ALA A 296 ASP A 298 5 3 HELIX 13 AB4 ALA A 314 ARG A 320 1 7 HELIX 14 AB5 ASN A 344 GLY A 359 1 16 HELIX 15 AB6 TYR A 377 ARG A 389 1 13 HELIX 16 AB7 THR A 399 THR A 413 1 15 HELIX 17 AB8 PRO A 416 ILE A 420 5 5 HELIX 18 AB9 GLY A 458 LEU A 468 1 11 HELIX 19 AC1 LEU A 504 ALA A 521 1 18 HELIX 20 AC2 ASP A 525 TYR A 545 1 21 HELIX 21 AC3 ARG B 70 ASP B 72 5 3 HELIX 22 AC4 HIS B 83 GLY B 88 1 6 HELIX 23 AC5 ALA B 89 ARG B 97 1 9 HELIX 24 AC6 SER B 105 CYS B 116 1 12 HELIX 25 AC7 ASP B 184 GLY B 195 1 12 HELIX 26 AC8 SER B 214 ALA B 229 1 16 HELIX 27 AC9 ASN B 241 LEU B 255 1 15 HELIX 28 AD1 GLY B 263 LEU B 276 1 14 HELIX 29 AD2 ASP B 288 MET B 295 1 8 HELIX 30 AD3 ALA B 296 GLN B 299 5 4 HELIX 31 AD4 SER B 313 SER B 319 1 7 HELIX 32 AD5 ASN B 344 GLY B 359 1 16 HELIX 33 AD6 GLY B 379 ARG B 389 1 11 HELIX 34 AD7 THR B 399 THR B 413 1 15 HELIX 35 AD8 GLY B 458 LEU B 468 1 11 HELIX 36 AD9 ASP B 500 ALA B 503 5 4 HELIX 37 AE1 LEU B 504 ALA B 520 1 17 HELIX 38 AE2 ASP B 525 ARG B 546 1 22 SHEET 1 AA1 8 VAL A 124 GLU A 127 0 SHEET 2 AA1 8 PRO A 101 GLY A 104 1 N GLY A 104 O VAL A 126 SHEET 3 AA1 8 ILE A 74 VAL A 78 1 N LEU A 77 O VAL A 103 SHEET 4 AA1 8 ARG A 39 ILE A 43 1 N LEU A 40 O GLU A 75 SHEET 5 AA1 8 THR A 32 HIS A 36 -1 N PHE A 34 O LEU A 41 SHEET 6 AA1 8 LEU A 16 ALA A 20 -1 N ARG A 17 O GLU A 35 SHEET 7 AA1 8 VAL A 427 LEU A 431 -1 O LEU A 431 N LEU A 16 SHEET 8 AA1 8 ILE A 438 ALA A 441 -1 O GLY A 440 N SER A 428 SHEET 1 AA2 3 ILE A 60 LEU A 61 0 SHEET 2 AA2 3 MET A 447 ASP A 450 -1 O MET A 447 N LEU A 61 SHEET 3 AA2 3 ILE A 453 ALA A 454 -1 O ILE A 453 N ASP A 450 SHEET 1 AA3 6 SER A 133 HIS A 136 0 SHEET 2 AA3 6 PHE A 139 ALA A 145 -1 O CYS A 141 N THR A 134 SHEET 3 AA3 6 LEU A 154 THR A 160 -1 O ALA A 155 N PHE A 144 SHEET 4 AA3 6 GLY A 163 HIS A 167 -1 O HIS A 167 N ILE A 156 SHEET 5 AA3 6 LEU A 198 ASP A 202 1 O LEU A 200 N LEU A 166 SHEET 6 AA3 6 VAL A 393 VAL A 396 1 O VAL A 396 N CYS A 201 SHEET 1 AA4 5 ARG A 258 VAL A 262 0 SHEET 2 AA4 5 VAL A 300 THR A 304 1 O ILE A 303 N SER A 260 SHEET 3 AA4 5 VAL A 233 ALA A 236 1 N VAL A 233 O LEU A 302 SHEET 4 AA4 5 LEU A 333 LEU A 336 1 O VAL A 335 N ILE A 234 SHEET 5 AA4 5 ARG A 361 VAL A 363 1 O ARG A 361 N ILE A 334 SHEET 1 AA5 3 HIS A 491 HIS A 493 0 SHEET 2 AA5 3 PHE A 472 VAL A 479 -1 N ALA A 474 O HIS A 493 SHEET 3 AA5 3 MET A 550 GLU A 557 1 O MET A 550 N VAL A 473 SHEET 1 AA6 8 VAL B 124 GLU B 127 0 SHEET 2 AA6 8 PRO B 101 GLY B 104 1 N VAL B 102 O VAL B 124 SHEET 3 AA6 8 ILE B 74 VAL B 78 1 N LEU B 77 O VAL B 103 SHEET 4 AA6 8 ARG B 39 ILE B 43 1 N ILE B 42 O VAL B 78 SHEET 5 AA6 8 THR B 32 HIS B 36 -1 N PHE B 34 O LEU B 41 SHEET 6 AA6 8 LEU B 16 ALA B 20 -1 N THR B 19 O VAL B 33 SHEET 7 AA6 8 VAL B 427 VAL B 432 -1 O VAL B 429 N VAL B 18 SHEET 8 AA6 8 LYS B 435 ALA B 441 -1 O SER B 437 N ASP B 430 SHEET 1 AA7 2 LEU B 59 LEU B 61 0 SHEET 2 AA7 2 MET B 447 VAL B 449 -1 O MET B 447 N LEU B 61 SHEET 1 AA8 6 SER B 133 HIS B 136 0 SHEET 2 AA8 6 PHE B 139 VAL B 146 -1 O CYS B 141 N THR B 134 SHEET 3 AA8 6 ALA B 153 THR B 160 -1 O TYR B 159 N GLU B 140 SHEET 4 AA8 6 GLY B 163 HIS B 167 -1 O HIS B 167 N ILE B 156 SHEET 5 AA8 6 LEU B 198 ASP B 202 1 O LEU B 200 N LEU B 166 SHEET 6 AA8 6 VAL B 393 VAL B 396 1 O MET B 394 N LEU B 199 SHEET 1 AA9 5 VAL B 259 PHE B 261 0 SHEET 2 AA9 5 VAL B 301 THR B 304 1 O ILE B 303 N SER B 260 SHEET 3 AA9 5 VAL B 233 ALA B 236 1 N VAL B 235 O LEU B 302 SHEET 4 AA9 5 LEU B 333 LEU B 336 1 O LEU B 333 N ILE B 234 SHEET 5 AA9 5 ARG B 361 VAL B 363 1 O VAL B 363 N ILE B 334 SHEET 1 AB1 3 HIS B 493 ARG B 495 0 SHEET 2 AB1 3 PHE B 472 VAL B 479 -1 N PHE B 472 O ARG B 495 SHEET 3 AB1 3 MET B 550 GLU B 557 1 O VAL B 552 N VAL B 473 LINK NE2 HIS A 81 ZN ZN A 601 1555 1555 2.41 LINK NE2 HIS A 83 ZN ZN A 601 1555 1555 2.41 LINK NE2 HIS A 86 ZN ZN A 602 1555 1555 2.63 LINK NE2 HIS A 148 ZN ZN A 601 1555 1555 1.83 LINK OD2 ASP A 170 ZN ZN A 601 1555 1555 1.76 LINK NE2 HIS A 397 ZN ZN A 602 1555 1555 2.20 LINK ZN ZN A 602 OP2 A C 2 1555 1555 1.94 LINK NE2 HIS B 81 ZN ZN B 602 1555 1555 2.14 LINK NE2 HIS B 83 ZN ZN B 602 1555 1555 1.94 LINK NE2 HIS B 86 ZN ZN B 601 1555 1555 2.21 LINK OD2 ASP B 170 ZN ZN B 601 1555 1555 2.05 LINK OD2 ASP B 170 ZN ZN B 602 1555 1555 1.91 LINK NE2 HIS B 397 ZN ZN B 601 1555 1555 2.16 LINK ZN ZN B 601 OP2 A D 2 1555 1555 2.21 CRYST1 92.060 145.380 192.100 90.00 90.00 90.00 C 2 2 21 16 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 0.010862 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005206 0.00000