HEADER LIGASE 07-NOV-18 6N0V TITLE TRNA LIGASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 6.5.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS SOURCE 3 144.50 / IMI 039719); SOURCE 4 ORGANISM_TAXID: 759272; SOURCE 5 STRAIN: DSM 1495 / CBS 144.50 / IMI 039719; SOURCE 6 GENE: CTHT_0034810; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRNA, RNA LIGASE, NUCLEOTIDYLTRANSFERASE, N6-AMP-LYSINE INTERMEDIATE, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BANERJEE,Y.GOLDGUR,S.SHUMAN REVDAT 3 04-DEC-19 6N0V 1 REMARK REVDAT 2 03-JUL-19 6N0V 1 JRNL REVDAT 1 09-JAN-19 6N0V 0 JRNL AUTH A.BANERJEE,S.GHOSH,Y.GOLDGUR,S.SHUMAN JRNL TITL STRUCTURE AND TWO-METAL MECHANISM OF FUNGAL TRNA LIGASE. JRNL REF NUCLEIC ACIDS RES. V. 47 1428 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30590734 JRNL DOI 10.1093/NAR/GKY1275 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 75283 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 3846 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 46.4905 - 7.4969 0.92 2551 144 0.1974 0.1951 REMARK 3 2 7.4969 - 5.9545 0.95 2697 146 0.2028 0.3034 REMARK 3 3 5.9545 - 5.2029 0.97 2676 147 0.1915 0.2098 REMARK 3 4 5.2029 - 4.7277 0.97 2738 151 0.1746 0.2055 REMARK 3 5 4.7277 - 4.3891 0.98 2721 145 0.1756 0.2410 REMARK 3 6 4.3891 - 4.1305 0.94 2647 144 0.1754 0.2373 REMARK 3 7 4.1305 - 3.9238 0.85 2365 126 0.1845 0.2114 REMARK 3 8 3.9238 - 3.7530 0.95 2665 140 0.1918 0.2147 REMARK 3 9 3.7530 - 3.6086 0.96 2652 139 0.1898 0.2529 REMARK 3 10 3.6086 - 3.4841 0.96 2731 147 0.1981 0.2302 REMARK 3 11 3.4841 - 3.3752 0.97 2717 148 0.2016 0.2600 REMARK 3 12 3.3752 - 3.2788 0.98 2746 149 0.2095 0.2489 REMARK 3 13 3.2788 - 3.1925 0.98 2712 145 0.2107 0.2260 REMARK 3 14 3.1925 - 3.1146 0.97 2687 144 0.2276 0.3034 REMARK 3 15 3.1146 - 3.0438 0.97 2734 148 0.2340 0.3121 REMARK 3 16 3.0438 - 2.9791 0.98 2711 144 0.2465 0.2820 REMARK 3 17 2.9791 - 2.9195 0.98 2714 146 0.2568 0.3090 REMARK 3 18 2.9195 - 2.8644 0.97 2713 145 0.2618 0.3187 REMARK 3 19 2.8644 - 2.8132 0.90 2510 138 0.2693 0.2970 REMARK 3 20 2.8132 - 2.7656 0.85 2382 129 0.2778 0.3642 REMARK 3 21 2.7656 - 2.7210 0.92 2580 136 0.2912 0.3567 REMARK 3 22 2.7210 - 2.6791 0.95 2645 144 0.2856 0.3084 REMARK 3 23 2.6791 - 2.6397 0.95 2665 141 0.2929 0.3646 REMARK 3 24 2.6397 - 2.6025 0.95 2632 145 0.3006 0.3372 REMARK 3 25 2.6025 - 2.5674 0.96 2712 141 0.3164 0.3836 REMARK 3 26 2.5674 - 2.5340 0.95 2621 140 0.3281 0.3952 REMARK 3 27 2.5340 - 2.5023 0.90 2513 134 0.3322 0.3977 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.120 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 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 : 0.010 6506 REMARK 3 ANGLE : 1.235 8792 REMARK 3 CHIRALITY : 0.067 932 REMARK 3 PLANARITY : 0.008 1130 REMARK 3 DIHEDRAL : 6.152 3890 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 13 THROUGH 407) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0936 47.0314 47.8110 REMARK 3 T TENSOR REMARK 3 T11: 0.4078 T22: 0.3464 REMARK 3 T33: 0.4161 T12: 0.0858 REMARK 3 T13: -0.0159 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 3.7708 L22: 0.6960 REMARK 3 L33: 1.0788 L12: -0.7272 REMARK 3 L13: 0.6334 L23: -0.0793 REMARK 3 S TENSOR REMARK 3 S11: -0.2468 S12: -0.2958 S13: 0.0064 REMARK 3 S21: 0.0944 S22: 0.1668 S23: 0.2620 REMARK 3 S31: -0.1236 S32: -0.2972 S33: 0.0665 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 13 THROUGH 407) REMARK 3 ORIGIN FOR THE GROUP (A): 55.2095 27.9361 47.5614 REMARK 3 T TENSOR REMARK 3 T11: 0.3536 T22: 0.2715 REMARK 3 T33: 0.1828 T12: 0.0174 REMARK 3 T13: 0.0118 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 3.4201 L22: 0.6110 REMARK 3 L33: 0.7559 L12: -0.2633 REMARK 3 L13: -0.3710 L23: 0.0315 REMARK 3 S TENSOR REMARK 3 S11: -0.0738 S12: 0.0380 S13: 0.0428 REMARK 3 S21: -0.0040 S22: 0.0549 S23: -0.0389 REMARK 3 S31: 0.0420 S32: 0.0787 S33: 0.0147 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 6N0V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000237984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-18 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39376 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 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 : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRIMETHYL N-OXIDE, 0.1 M TRIS PH REMARK 280 8.5, 20% (W/V) PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 77.61550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.03550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.61550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.03550 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLY A 3 REMARK 465 THR A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 6 REMARK 465 LYS A 7 REMARK 465 GLN A 8 REMARK 465 ARG A 9 REMARK 465 ASP A 10 REMARK 465 SER A 11 REMARK 465 LEU A 12 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 GLY B 3 REMARK 465 THR B 4 REMARK 465 ALA B 5 REMARK 465 GLU B 6 REMARK 465 LYS B 7 REMARK 465 GLN B 8 REMARK 465 ARG B 9 REMARK 465 ASP B 10 REMARK 465 SER B 11 REMARK 465 LEU B 12 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 O HOH B 604 O HOH B 624 1.85 REMARK 500 NH2 ARG B 99 O HOH B 601 2.01 REMARK 500 ND2 ASN A 382 O HOH A 601 2.02 REMARK 500 O HOH B 609 O HOH B 616 2.05 REMARK 500 O PRO B 373 N ALA B 376 2.11 REMARK 500 OH TYR A 379 O HOH A 602 2.11 REMARK 500 OE1 GLU A 290 O HOH A 603 2.13 REMARK 500 OE1 GLU A 207 O HOH A 604 2.15 REMARK 500 NZ LYS A 387 O HOH A 605 2.16 REMARK 500 NE2 GLN A 39 O GLY B 315 2.17 REMARK 500 O GLY B 151 O HOH B 602 2.19 REMARK 500 OE1 GLU B 160 O HOH B 603 2.19 REMARK 500 OE2 GLU B 300 NZ LYS B 325 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 ARG A 67 NZ LYS B 53 4556 2.00 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 GLU A 327 CA - CB - CG ANGL. DEV. = 13.4 DEGREES REMARK 500 LYS B 53 CB - CG - CD ANGL. DEV. = -20.0 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 ARG A 15 35.36 -80.13 REMARK 500 SER A 58 -161.06 -110.92 REMARK 500 ARG A 99 -77.92 -87.08 REMARK 500 ASP A 125 -2.12 73.89 REMARK 500 HIS A 170 -5.79 74.18 REMARK 500 PHE A 224 -64.65 -96.53 REMARK 500 HIS A 227 -130.40 -102.04 REMARK 500 CYS A 306 -175.22 -171.64 REMARK 500 PRO A 312 9.50 -62.77 REMARK 500 TYR A 317 83.23 -153.57 REMARK 500 ARG B 15 44.80 -91.93 REMARK 500 SER B 58 -158.47 -109.33 REMARK 500 ASP B 125 -5.60 74.11 REMARK 500 ASP B 221 117.47 -164.28 REMARK 500 PHE B 224 -63.34 -90.66 REMARK 500 HIS B 227 -129.41 -99.59 REMARK 500 LYS B 235 -25.52 66.21 REMARK 500 ASN B 380 109.76 -53.97 REMARK 500 GLN B 381 -74.27 66.72 REMARK 500 ASN B 382 -67.80 -94.13 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 PHE A 326 GLU A 327 -148.40 REMARK 500 GLN A 381 ASN A 382 -136.12 REMARK 500 ASN B 382 HIS B 383 -147.05 REMARK 500 ASN B 405 LEU B 406 145.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 693 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH B 694 DISTANCE = 7.68 ANGSTROMS 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 APK A 148 O2P REMARK 620 2 HOH A 632 O 71.9 REMARK 620 3 HOH A 628 O 101.5 79.9 REMARK 620 4 HOH A 633 O 139.3 74.7 94.8 REMARK 620 5 HOH A 645 O 82.4 62.1 138.7 61.5 REMARK 620 6 HOH A 646 O 94.4 148.6 131.3 102.4 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 APK B 148 O2P REMARK 620 2 HOH B 618 O 73.0 REMARK 620 3 HOH B 632 O 158.5 87.3 REMARK 620 4 HOH B 642 O 108.5 175.6 90.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 501 DBREF 6N0V A 1 407 UNP G0S6G2 G0S6G2_CHATD 1 407 DBREF 6N0V B 1 407 UNP G0S6G2 G0S6G2_CHATD 1 407 SEQRES 1 A 407 MET ASP GLY THR ALA GLU LYS GLN ARG ASP SER LEU ALA SEQRES 2 A 407 SER ARG TYR LYS ALA SER THR ASP TYR ALA LYS ASP ALA SEQRES 3 A 407 GLU GLY LEU THR ALA PRO TYR VAL SER GLN ASP PRO GLN SEQRES 4 A 407 GLU THR ALA ALA LEU VAL ARG ALA LEU ASP ASP ALA ALA SEQRES 5 A 407 LYS LYS GLY LYS LYS SER GLY GLY PHE SER VAL LYS LYS SEQRES 6 A 407 THR ARG TYR ALA VAL ALA SER SER PRO THR GLY ALA GLU SEQRES 7 A 407 VAL ASP SER TRP ARG PHE ASN ASP TRP ASP TYR LYS LYS SEQRES 8 A 407 PRO ASP LEU PRO THR TYR ALA ARG GLY LEU PHE THR THR SEQRES 9 A 407 ARG THR GLN HIS GLY VAL PRO GLU ILE ALA VAL ARG GLY SEQRES 10 A 407 TYR ASP LYS PHE PHE ASN ILE ASP GLU THR ARG ASP THR SEQRES 11 A 407 ALA TRP SER ALA ILE ARG GLU ARG THR LYS GLY PRO TYR SEQRES 12 A 407 GLU LEU THR LEU APK GLU ASN GLY CYS ILE ILE PHE ILE SEQRES 13 A 407 SER GLY LEU GLU ASP GLY THR LEU LEU VAL CYS SER LYS SEQRES 14 A 407 HIS SER THR GLY ASP ARG SER ASP VAL ALA LEU SER HIS SEQRES 15 A 407 SER SER ALA GLY GLU LYS HIS LEU GLU ALA GLN LEU GLU SEQRES 16 A 407 ARG ILE GLY LYS THR LYS GLU GLU LEU ALA ARG GLU LEU SEQRES 17 A 407 ARG LYS ARG ASN ALA THR ALA VAL ALA GLU LEU CYS ASP SEQRES 18 A 407 ASP SER PHE GLU GLU HIS ILE LEU ALA TYR GLY PRO ASP SEQRES 19 A 407 LYS ALA GLY LEU TYR LEU HIS GLY ILE ASN LEU ASN ILE SEQRES 20 A 407 PRO GLU PHE ILE THR TYR PRO SER PRO LEU VAL GLN LYS SEQRES 21 A 407 PHE ALA GLU ASP TRP GLY PHE ARG LYS THR GLY LEU ILE SEQRES 22 A 407 ILE ILE ASP ASN ILE ASP ASP VAL LYS ALA PHE LEU GLU SEQRES 23 A 407 GLU VAL ALA GLU THR GLY ALA HIS ASP GLY ARG ASP VAL SEQRES 24 A 407 GLU GLY PHE VAL ILE ARG CYS LYS LYS SER THR ASN PRO SEQRES 25 A 407 GLY VAL GLY PRO TYR HIS ASP TRP PHE PHE LYS TYR LYS SEQRES 26 A 407 PHE GLU GLU PRO TYR LEU MET TYR ARG GLN TRP ARG GLU SEQRES 27 A 407 CYS THR LYS ALA LEU ILE SER GLY LYS GLN PRO LYS ILE SEQRES 28 A 407 LYS LYS HIS VAL LYS ILE THR GLU GLU TYR LEU LEU TYR SEQRES 29 A 407 ALA ARG LYS ARG LEU ALA ALA ASP PRO LYS LEU ALA LYS SEQRES 30 A 407 LEU TYR ASN GLN ASN HIS GLY ILE ILE LYS LEU ARG ASN SEQRES 31 A 407 ASP PHE LEU GLU TYR LYS ASN MET LYS GLY THR ASP ALA SEQRES 32 A 407 ALA ASN LEU GLU SEQRES 1 B 407 MET ASP GLY THR ALA GLU LYS GLN ARG ASP SER LEU ALA SEQRES 2 B 407 SER ARG TYR LYS ALA SER THR ASP TYR ALA LYS ASP ALA SEQRES 3 B 407 GLU GLY LEU THR ALA PRO TYR VAL SER GLN ASP PRO GLN SEQRES 4 B 407 GLU THR ALA ALA LEU VAL ARG ALA LEU ASP ASP ALA ALA SEQRES 5 B 407 LYS LYS GLY LYS LYS SER GLY GLY PHE SER VAL LYS LYS SEQRES 6 B 407 THR ARG TYR ALA VAL ALA SER SER PRO THR GLY ALA GLU SEQRES 7 B 407 VAL ASP SER TRP ARG PHE ASN ASP TRP ASP TYR LYS LYS SEQRES 8 B 407 PRO ASP LEU PRO THR TYR ALA ARG GLY LEU PHE THR THR SEQRES 9 B 407 ARG THR GLN HIS GLY VAL PRO GLU ILE ALA VAL ARG GLY SEQRES 10 B 407 TYR ASP LYS PHE PHE ASN ILE ASP GLU THR ARG ASP THR SEQRES 11 B 407 ALA TRP SER ALA ILE ARG GLU ARG THR LYS GLY PRO TYR SEQRES 12 B 407 GLU LEU THR LEU APK GLU ASN GLY CYS ILE ILE PHE ILE SEQRES 13 B 407 SER GLY LEU GLU ASP GLY THR LEU LEU VAL CYS SER LYS SEQRES 14 B 407 HIS SER THR GLY ASP ARG SER ASP VAL ALA LEU SER HIS SEQRES 15 B 407 SER SER ALA GLY GLU LYS HIS LEU GLU ALA GLN LEU GLU SEQRES 16 B 407 ARG ILE GLY LYS THR LYS GLU GLU LEU ALA ARG GLU LEU SEQRES 17 B 407 ARG LYS ARG ASN ALA THR ALA VAL ALA GLU LEU CYS ASP SEQRES 18 B 407 ASP SER PHE GLU GLU HIS ILE LEU ALA TYR GLY PRO ASP SEQRES 19 B 407 LYS ALA GLY LEU TYR LEU HIS GLY ILE ASN LEU ASN ILE SEQRES 20 B 407 PRO GLU PHE ILE THR TYR PRO SER PRO LEU VAL GLN LYS SEQRES 21 B 407 PHE ALA GLU ASP TRP GLY PHE ARG LYS THR GLY LEU ILE SEQRES 22 B 407 ILE ILE ASP ASN ILE ASP ASP VAL LYS ALA PHE LEU GLU SEQRES 23 B 407 GLU VAL ALA GLU THR GLY ALA HIS ASP GLY ARG ASP VAL SEQRES 24 B 407 GLU GLY PHE VAL ILE ARG CYS LYS LYS SER THR ASN PRO SEQRES 25 B 407 GLY VAL GLY PRO TYR HIS ASP TRP PHE PHE LYS TYR LYS SEQRES 26 B 407 PHE GLU GLU PRO TYR LEU MET TYR ARG GLN TRP ARG GLU SEQRES 27 B 407 CYS THR LYS ALA LEU ILE SER GLY LYS GLN PRO LYS ILE SEQRES 28 B 407 LYS LYS HIS VAL LYS ILE THR GLU GLU TYR LEU LEU TYR SEQRES 29 B 407 ALA ARG LYS ARG LEU ALA ALA ASP PRO LYS LEU ALA LYS SEQRES 30 B 407 LEU TYR ASN GLN ASN HIS GLY ILE ILE LYS LEU ARG ASN SEQRES 31 B 407 ASP PHE LEU GLU TYR LYS ASN MET LYS GLY THR ASP ALA SEQRES 32 B 407 ALA ASN LEU GLU MODRES 6N0V APK A 148 LYS MODIFIED RESIDUE MODRES 6N0V APK B 148 LYS MODIFIED RESIDUE HET APK A 148 31 HET APK B 148 31 HET MN A 501 1 HET MN B 501 1 HETNAM APK 5'-O-[(S)-{[(5S)-5-AMINO-6-OXOHEXYL]AMINO}(HYDROXY) HETNAM 2 APK PHOSPHORYL]ADENOSINE HETNAM MN MANGANESE (II) ION FORMUL 1 APK 2(C16 H26 N7 O7 P) FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *148(H2 O) HELIX 1 AA1 TYR A 22 LEU A 29 5 8 HELIX 2 AA2 ASP A 37 ALA A 52 1 16 HELIX 3 AA3 ASP A 86 LYS A 91 5 6 HELIX 4 AA4 ALA A 131 ARG A 138 1 8 HELIX 5 AA5 SER A 181 ILE A 197 1 17 HELIX 6 AA6 THR A 200 ARG A 211 1 12 HELIX 7 AA7 PRO A 254 GLY A 266 1 13 HELIX 8 AA8 ASN A 277 ALA A 289 1 13 HELIX 9 AA9 PRO A 329 SER A 345 1 17 HELIX 10 AB1 HIS A 354 ASP A 372 1 19 HELIX 11 AB2 ASP A 372 TYR A 379 1 8 HELIX 12 AB3 GLY A 384 LYS A 396 1 13 HELIX 13 AB4 LYS A 399 ASN A 405 1 7 HELIX 14 AB5 LYS B 24 LEU B 29 5 6 HELIX 15 AB6 ASP B 37 ALA B 52 1 16 HELIX 16 AB7 ASP B 86 LYS B 91 5 6 HELIX 17 AB8 ALA B 131 ARG B 138 1 8 HELIX 18 AB9 SER B 181 ILE B 197 1 17 HELIX 19 AC1 THR B 200 ARG B 211 1 12 HELIX 20 AC2 PRO B 254 GLY B 266 1 13 HELIX 21 AC3 ASN B 277 ALA B 289 1 13 HELIX 22 AC4 PRO B 329 SER B 345 1 17 HELIX 23 AC5 HIS B 354 ASP B 372 1 19 HELIX 24 AC6 LYS B 374 TYR B 379 1 6 HELIX 25 AC7 GLY B 384 LYS B 396 1 13 HELIX 26 AC8 LYS B 399 ALA B 404 1 6 SHEET 1 AA1 4 VAL A 63 ALA A 69 0 SHEET 2 AA1 4 GLU A 78 PHE A 84 -1 O SER A 81 N THR A 66 SHEET 3 AA1 4 LEU A 101 ARG A 105 -1 O THR A 103 N ASP A 80 SHEET 4 AA1 4 PRO A 111 ARG A 116 -1 O GLU A 112 N THR A 104 SHEET 1 AA2 4 LEU A 272 ILE A 275 0 SHEET 2 AA2 4 THR A 139 LEU A 147 -1 N LEU A 145 O ILE A 273 SHEET 3 AA2 4 GLY A 301 LYS A 308 -1 O VAL A 303 N THR A 146 SHEET 4 AA2 4 HIS A 318 LYS A 325 -1 O TRP A 320 N CYS A 306 SHEET 1 AA3 5 LEU A 164 SER A 168 0 SHEET 2 AA3 5 CYS A 152 GLY A 158 -1 N PHE A 155 O CYS A 167 SHEET 3 AA3 5 ALA A 213 CYS A 220 -1 O LEU A 219 N CYS A 152 SHEET 4 AA3 5 GLY A 237 LEU A 245 -1 O TYR A 239 N GLU A 218 SHEET 5 AA3 5 ARG A 268 LYS A 269 1 O ARG A 268 N LEU A 240 SHEET 1 AA4 2 ALA A 293 HIS A 294 0 SHEET 2 AA4 2 ARG A 297 ASP A 298 -1 O ARG A 297 N HIS A 294 SHEET 1 AA5 4 VAL B 63 ALA B 69 0 SHEET 2 AA5 4 GLU B 78 PHE B 84 -1 O SER B 81 N THR B 66 SHEET 3 AA5 4 LEU B 101 ARG B 105 -1 O THR B 103 N ASP B 80 SHEET 4 AA5 4 PRO B 111 ARG B 116 -1 O GLU B 112 N THR B 104 SHEET 1 AA6 4 LEU B 272 ILE B 275 0 SHEET 2 AA6 4 THR B 139 LEU B 147 -1 N LEU B 145 O ILE B 273 SHEET 3 AA6 4 GLY B 301 LYS B 308 -1 O ARG B 305 N GLU B 144 SHEET 4 AA6 4 HIS B 318 LYS B 325 -1 O TRP B 320 N CYS B 306 SHEET 1 AA7 5 LEU B 164 CYS B 167 0 SHEET 2 AA7 5 CYS B 152 GLY B 158 -1 N PHE B 155 O CYS B 167 SHEET 3 AA7 5 ALA B 213 CYS B 220 -1 O LEU B 219 N CYS B 152 SHEET 4 AA7 5 GLY B 237 LEU B 245 -1 O GLY B 242 N VAL B 216 SHEET 5 AA7 5 ARG B 268 LYS B 269 1 O ARG B 268 N LEU B 240 SHEET 1 AA8 2 ALA B 293 HIS B 294 0 SHEET 2 AA8 2 ARG B 297 ASP B 298 -1 O ARG B 297 N HIS B 294 LINK C LEU A 147 N APK A 148 1555 1555 1.33 LINK C APK A 148 N GLU A 149 1555 1555 1.33 LINK O2P APK A 148 MN MN A 501 1555 1555 2.35 LINK C LEU B 147 N APK B 148 1555 1555 1.34 LINK C APK B 148 N GLU B 149 1555 1555 1.32 LINK O2P APK B 148 MN MN B 501 1555 1555 2.07 LINK MN MN A 501 O HOH A 632 1555 1555 2.44 LINK MN MN A 501 O HOH A 628 1555 1555 2.66 LINK MN MN A 501 O HOH A 633 1555 1555 2.21 LINK MN MN A 501 O HOH A 645 1555 1555 2.38 LINK MN MN A 501 O HOH A 646 1555 1555 2.26 LINK MN MN B 501 O HOH B 618 1555 1555 2.67 LINK MN MN B 501 O HOH B 632 1555 1555 2.40 LINK MN MN B 501 O HOH B 642 1555 1555 2.33 CISPEP 1 GLY A 141 PRO A 142 0 -0.38 CISPEP 2 GLU A 328 PRO A 329 0 8.54 CISPEP 3 GLY B 141 PRO B 142 0 0.64 CISPEP 4 GLU B 328 PRO B 329 0 7.20 SITE 1 AC1 6 APK A 148 HOH A 628 HOH A 632 HOH A 633 SITE 2 AC1 6 HOH A 645 HOH A 646 SITE 1 AC2 6 APK B 148 HOH B 611 HOH B 618 HOH B 632 SITE 2 AC2 6 HOH B 642 HOH B 689 CRYST1 155.231 114.071 68.200 90.00 100.36 90.00 C 1 2 1 8 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 0.006442 0.000000 0.001178 0.00000 SCALE2 0.000000 0.008766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014906 0.00000