HEADER LIGASE 12-FEB-20 6VTB TITLE NAEGLERIA GRUBERI RNA LIGASE K326A MUTANT WITH ATP AND MN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAEGLERIA GRUBERI; SOURCE 3 ORGANISM_COMMON: AMOEBA; SOURCE 4 ORGANISM_TAXID: 5762; SOURCE 5 GENE: NAEGRDRAFT_82186; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA REPAIR, ADENYLYLTRANSFERASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.C.UNCIULEAC,Y.GOLDGUR,S.SHUMAN REVDAT 4 11-OCT-23 6VTB 1 LINK REVDAT 3 10-JUN-20 6VTB 1 JRNL REVDAT 2 06-MAY-20 6VTB 1 JRNL REVDAT 1 08-APR-20 6VTB 0 JRNL AUTH M.C.UNCIULEAC,Y.GOLDGUR,S.SHUMAN JRNL TITL CAVEAT MUTATOR: ALANINE SUBSTITUTIONS FOR CONSERVED AMINO JRNL TITL 2 ACIDS IN RNA LIGASE ELICIT UNEXPECTED REARRANGEMENTS OF THE JRNL TITL 3 ACTIVE SITE FOR LYSINE ADENYLYLATION. JRNL REF NUCLEIC ACIDS RES. V. 48 5603 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32315072 JRNL DOI 10.1093/NAR/GKAA238 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 94052 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3770 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 28.6000 - 4.6341 1.00 3470 146 0.1416 0.1808 REMARK 3 2 4.6341 - 3.6807 0.82 2894 118 0.1282 0.1395 REMARK 3 3 3.6807 - 3.2161 0.92 3209 132 0.1335 0.1626 REMARK 3 4 3.2161 - 2.9224 1.00 3480 148 0.1498 0.1922 REMARK 3 5 2.9224 - 2.7131 1.00 3516 147 0.1536 0.1892 REMARK 3 6 2.7131 - 2.5532 0.99 3419 144 0.1596 0.1909 REMARK 3 7 2.5532 - 2.4254 0.98 3424 141 0.1632 0.1965 REMARK 3 8 2.4254 - 2.3199 0.98 3408 137 0.1579 0.1950 REMARK 3 9 2.3199 - 2.2306 0.97 3403 144 0.1751 0.1866 REMARK 3 10 2.2306 - 2.1537 0.98 3412 140 0.1634 0.1879 REMARK 3 11 2.1537 - 2.0864 0.98 3410 142 0.1526 0.1604 REMARK 3 12 2.0864 - 2.0268 0.98 3403 145 0.1626 0.2341 REMARK 3 13 2.0268 - 1.9734 0.98 3386 146 0.1665 0.1918 REMARK 3 14 1.9734 - 1.9253 0.97 3436 150 0.1658 0.2178 REMARK 3 15 1.9253 - 1.8815 0.97 3338 140 0.1917 0.2319 REMARK 3 16 1.8815 - 1.8415 0.97 3422 146 0.1867 0.1902 REMARK 3 17 1.8415 - 1.8046 0.96 3344 138 0.1810 0.2123 REMARK 3 18 1.8046 - 1.7706 0.97 3308 136 0.1674 0.2270 REMARK 3 19 1.7706 - 1.7390 0.96 3382 139 0.1838 0.2300 REMARK 3 20 1.7390 - 1.7095 0.96 3347 138 0.1855 0.1690 REMARK 3 21 1.7095 - 1.6819 0.95 3342 137 0.1886 0.2073 REMARK 3 22 1.6819 - 1.6561 0.96 3313 139 0.1955 0.2702 REMARK 3 23 1.6561 - 1.6317 0.94 3354 139 0.2007 0.2685 REMARK 3 24 1.6317 - 1.6087 0.97 3332 141 0.2139 0.2356 REMARK 3 25 1.6087 - 1.5870 0.94 3309 139 0.2269 0.2761 REMARK 3 26 1.5870 - 1.5664 0.96 3292 137 0.2387 0.2696 REMARK 3 27 1.5664 - 1.5470 0.83 2929 121 0.2590 0.2748 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.79 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 0 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.1580 67.4552 122.9908 REMARK 3 T TENSOR REMARK 3 T11: 0.0579 T22: 0.0754 REMARK 3 T33: 0.0690 T12: -0.0011 REMARK 3 T13: -0.0041 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.2397 L22: 0.2165 REMARK 3 L33: 0.2255 L12: -0.0124 REMARK 3 L13: -0.1027 L23: 0.0453 REMARK 3 S TENSOR REMARK 3 S11: 0.0017 S12: -0.0364 S13: -0.0090 REMARK 3 S21: 0.0282 S22: -0.0229 S23: 0.0167 REMARK 3 S31: 0.0042 S32: -0.0591 S33: -0.0193 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 120 THROUGH 339 ) REMARK 3 ORIGIN FOR THE GROUP (A): 64.1722 64.4690 107.2033 REMARK 3 T TENSOR REMARK 3 T11: 0.0473 T22: 0.0428 REMARK 3 T33: 0.0405 T12: -0.0075 REMARK 3 T13: -0.0007 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.4937 L22: 0.2464 REMARK 3 L33: 0.4155 L12: 0.0672 REMARK 3 L13: -0.2469 L23: 0.0570 REMARK 3 S TENSOR REMARK 3 S11: -0.0022 S12: 0.0620 S13: 0.0012 REMARK 3 S21: -0.0258 S22: 0.0292 S23: -0.0116 REMARK 3 S31: -0.0240 S32: -0.0539 S33: 0.0001 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 6VTB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000247048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-15 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.547 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.91400 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: 5COT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NGRRNLK326A (21.4 MG/ML) WAS ADJUSTED REMARK 280 TO 2 MM ATP AND 5 MM MNCL2 AND INCUBATED FOR 15 MIN ON ICE REMARK 280 BEFORE ALIQUOTS OF THE PROTEIN SOLUTION (1 UL) WERE MIXED ON A REMARK 280 COVERSLIP WITH AN EQUAL VOLUME OF PRECIPITANT SOLUTION REMARK 280 CONTAINING 0.1 M HEPES PH 6.5, 30% PEG6000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.51550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.94400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.11050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.94400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.51550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.11050 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: 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 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 76 O HOH A 501 2.10 REMARK 500 O HOH A 520 O HOH A 523 2.11 REMARK 500 NH1 ARG A 149 O HOH A 502 2.14 REMARK 500 O HOH A 954 O HOH A 1112 2.14 REMARK 500 O HOH A 793 O HOH A 949 2.14 REMARK 500 O HOH A 660 O HOH A 937 2.16 REMARK 500 O HOH A 716 O HOH A 1014 2.16 REMARK 500 O HOH A 621 O HOH A 952 2.17 REMARK 500 O HOH A 754 O HOH A 913 2.18 REMARK 500 O HOH A 617 O HOH A 932 2.18 REMARK 500 O HOH A 538 O HOH A 696 2.18 REMARK 500 O HOH A 544 O HOH A 1016 2.19 REMARK 500 O HOH A 547 O HOH A 1075 2.19 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 30 -129.10 52.00 REMARK 500 ASP A 53 -9.20 84.81 REMARK 500 ASP A 182 -119.23 55.86 REMARK 500 ASN A 290 53.47 -148.99 REMARK 500 HIS A 336 76.85 -109.31 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 A1202 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1203 DISTANCE = 6.14 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 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 123 OE1 REMARK 620 2 GLU A 123 OE2 50.7 REMARK 620 3 ATP A 401 O2G 87.2 89.5 REMARK 620 4 HOH A 527 O 108.0 59.5 76.0 REMARK 620 5 HOH A 531 O 159.8 148.5 97.0 92.2 REMARK 620 6 HOH A 545 O 92.5 88.0 176.9 101.2 84.3 REMARK 620 7 HOH A 725 O 94.9 145.4 84.4 148.7 66.1 98.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 401 O3G REMARK 620 2 ATP A 401 O2B 86.1 REMARK 620 3 HOH A 563 O 91.4 96.2 REMARK 620 4 HOH A 624 O 91.0 176.6 85.7 REMARK 620 5 HOH A 631 O 177.1 93.1 85.9 89.9 REMARK 620 6 HOH A 755 O 95.5 89.2 171.5 89.3 87.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 401 O1B REMARK 620 2 ATP A 401 O2A 94.2 REMARK 620 3 HOH A 506 O 89.4 168.4 REMARK 620 4 HOH A 596 O 74.8 93.9 97.7 REMARK 620 5 HOH A 797 O 109.7 82.3 86.1 174.2 REMARK 620 6 HOH A 819 O 150.2 78.2 103.9 77.0 97.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 404 DBREF 6VTB A 1 339 UNP D2W2Z5 D2W2Z5_NAEGR 1 339 SEQADV 6VTB SER A 0 UNP D2W2Z5 EXPRESSION TAG SEQADV 6VTB ALA A 326 UNP D2W2Z5 LYS 326 ENGINEERED MUTATION SEQRES 1 A 340 SER MET GLY VAL ARG LYS LEU ALA THR ILE ARG THR ALA SEQRES 2 A 340 GLY GLU ILE THR PRO ILE ALA GLY ALA GLU ALA ILE GLU SEQRES 3 A 340 CYS CYS HIS VAL ASP GLY TRP THR CYS VAL ILE LYS LYS SEQRES 4 A 340 GLY GLU PHE LYS GLN GLY ASP ARG GLY VAL TYR PHE GLU SEQRES 5 A 340 ILE ASP SER PHE ILE LYS GLU ASP ASN ASP ARG TYR PRO SEQRES 6 A 340 MET LEU SER LYS GLN VAL ILE ASP TYR GLU GLY GLN ARG SEQRES 7 A 340 GLY THR ARG LEU ARG THR ALA ARG LEU ARG GLY GLN LEU SEQRES 8 A 340 SER GLN GLY LEU PHE LEU PRO MET ASP ARG PHE PRO GLU SEQRES 9 A 340 LEU ALA SER ASN GLN VAL GLY ASP ASP VAL THR GLU ILE SEQRES 10 A 340 LEU GLY ILE THR LYS TRP GLU PRO PRO ILE SER THR ASN SEQRES 11 A 340 LEU SER GLY GLU ILE LEU GLY GLU PHE PRO THR PHE ILE SEQRES 12 A 340 SER LYS THR ASP GLN GLU ARG VAL GLN ASN LEU ILE PRO SEQRES 13 A 340 GLN ILE GLU GLU ASN LYS GLY GLN LYS PHE GLU VAL THR SEQRES 14 A 340 VAL LYS LEU ASP GLY SER SER MET THR VAL TYR ARG LYS SEQRES 15 A 340 ASP ASP HIS ILE GLY VAL CYS GLY ARG ASN TRP GLU LEU SEQRES 16 A 340 ARG GLU THR ALA THR ASN ALA GLN TRP HIS ALA ALA ARG SEQRES 17 A 340 ARG ASN LYS MET ILE GLU GLY LEU GLN PHE LEU ASN ARG SEQRES 18 A 340 ASN LEU ALA LEU GLN GLY GLU ILE ILE GLY GLU SER ILE SEQRES 19 A 340 GLN GLY ASN LEU GLU LYS LEU LYS GLY GLN ASP PHE TYR SEQRES 20 A 340 LEU PHE ASP ILE TYR ASP ILE ASP LYS ALA GLN TYR LEU SEQRES 21 A 340 THR PRO ILE GLU ARG GLN SER LEU VAL LYS GLN LEU ASN SEQRES 22 A 340 ASP ASN GLY PHE THR VAL LYS HIS VAL PRO ILE LEU ASP SEQRES 23 A 340 ASP LEU GLU LEU ASN HIS THR ALA GLU GLN ILE LEU ALA SEQRES 24 A 340 MET ALA ASP GLY PRO SER LEU ASN LYS ASN VAL LYS ARG SEQRES 25 A 340 GLU GLY LEU VAL PHE LYS ARG LEU ASP GLY LYS PHE SER SEQRES 26 A 340 PHE ALA ALA ILE SER ASN ALA TYR LEU GLU LYS HIS LYS SEQRES 27 A 340 ASP ARG HET ATP A 401 31 HET MN A 402 1 HET MN A 403 1 HET MN A 404 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 MN 3(MN 2+) FORMUL 6 HOH *703(H2 O) HELIX 1 AA1 TYR A 63 SER A 67 5 5 HELIX 2 AA2 ASP A 99 ALA A 105 5 7 HELIX 3 AA3 SER A 127 SER A 131 5 5 HELIX 4 AA4 ARG A 149 ASN A 152 5 4 HELIX 5 AA5 LEU A 153 ASN A 160 1 8 HELIX 6 AA6 ASN A 200 ASN A 209 1 10 HELIX 7 AA7 LYS A 210 ASN A 219 1 10 HELIX 8 AA8 THR A 260 ASN A 274 1 15 HELIX 9 AA9 THR A 292 ASP A 301 1 10 HELIX 10 AB1 SER A 329 HIS A 336 1 8 SHEET 1 AA1 3 ALA A 7 THR A 11 0 SHEET 2 AA1 3 ARG A 46 PHE A 50 -1 O TYR A 49 N THR A 8 SHEET 3 AA1 3 LEU A 94 PRO A 97 -1 O LEU A 94 N PHE A 50 SHEET 1 AA2 3 ILE A 15 PRO A 17 0 SHEET 2 AA2 3 ILE A 24 VAL A 29 -1 O CYS A 26 N THR A 16 SHEET 3 AA2 3 TRP A 32 LYS A 37 -1 O CYS A 34 N CYS A 27 SHEET 1 AA3 4 ILE A 71 TYR A 73 0 SHEET 2 AA3 4 GLN A 76 ARG A 80 -1 O GLY A 78 N ILE A 71 SHEET 3 AA3 4 SER A 54 LYS A 57 -1 N ILE A 56 O THR A 79 SHEET 4 AA3 4 THR A 120 LYS A 121 -1 O THR A 120 N PHE A 55 SHEET 1 AA4 2 ALA A 84 LEU A 86 0 SHEET 2 AA4 2 GLN A 89 SER A 91 -1 O SER A 91 N ALA A 84 SHEET 1 AA5 7 GLU A 133 GLU A 137 0 SHEET 2 AA5 7 TRP A 192 ARG A 195 -1 O ARG A 195 N GLU A 133 SHEET 3 AA5 7 HIS A 184 CYS A 188 -1 N VAL A 187 O LEU A 194 SHEET 4 AA5 7 SER A 174 LYS A 181 -1 N THR A 177 O CYS A 188 SHEET 5 AA5 7 LEU A 222 GLY A 230 -1 O LEU A 224 N VAL A 178 SHEET 6 AA5 7 GLN A 243 ASP A 252 -1 O PHE A 248 N GLN A 225 SHEET 7 AA5 7 GLN A 257 TYR A 258 -1 O GLN A 257 N ASP A 252 SHEET 1 AA6 7 GLU A 133 GLU A 137 0 SHEET 2 AA6 7 TRP A 192 ARG A 195 -1 O ARG A 195 N GLU A 133 SHEET 3 AA6 7 HIS A 184 CYS A 188 -1 N VAL A 187 O LEU A 194 SHEET 4 AA6 7 SER A 174 LYS A 181 -1 N THR A 177 O CYS A 188 SHEET 5 AA6 7 LEU A 222 GLY A 230 -1 O LEU A 224 N VAL A 178 SHEET 6 AA6 7 GLN A 243 ASP A 252 -1 O PHE A 248 N GLN A 225 SHEET 7 AA6 7 LYS A 279 HIS A 280 1 O LYS A 279 N LEU A 247 SHEET 1 AA7 4 LEU A 287 GLU A 288 0 SHEET 2 AA7 4 LYS A 164 LYS A 170 -1 N PHE A 165 O LEU A 287 SHEET 3 AA7 4 GLY A 313 ARG A 318 -1 O LYS A 317 N GLU A 166 SHEET 4 AA7 4 SER A 324 ILE A 328 -1 O PHE A 325 N PHE A 316 LINK OE1 GLU A 123 MN MN A 403 1555 1555 2.21 LINK OE2 GLU A 123 MN MN A 403 1555 1555 2.77 LINK O3G ATP A 401 MN MN A 402 1555 1555 2.15 LINK O2B ATP A 401 MN MN A 402 1555 1555 2.13 LINK O2G ATP A 401 MN MN A 403 1555 1555 2.08 LINK O1B ATP A 401 MN MN A 404 1555 1555 1.93 LINK O2A ATP A 401 MN MN A 404 1555 1555 2.21 LINK MN MN A 402 O HOH A 563 1555 1555 2.19 LINK MN MN A 402 O HOH A 624 1555 1555 2.17 LINK MN MN A 402 O HOH A 631 1555 1555 2.25 LINK MN MN A 402 O HOH A 755 1555 1555 2.24 LINK MN MN A 403 O HOH A 527 1555 1555 2.12 LINK MN MN A 403 O HOH A 531 1555 1555 2.12 LINK MN MN A 403 O HOH A 545 1555 1555 2.23 LINK MN MN A 403 O HOH A 725 1555 1555 2.06 LINK MN MN A 404 O HOH A 506 1555 1555 2.43 LINK MN MN A 404 O HOH A 596 1555 1555 2.39 LINK MN MN A 404 O HOH A 797 1555 1555 2.11 LINK MN MN A 404 O HOH A 819 1555 1555 2.34 SITE 1 AC1 35 GLU A 123 THR A 145 ASP A 146 GLN A 147 SITE 2 AC1 35 THR A 168 VAL A 169 LYS A 170 LEU A 171 SITE 3 AC1 35 SER A 175 ARG A 190 GLU A 227 PHE A 248 SITE 4 AC1 35 VAL A 281 VAL A 315 LYS A 317 MN A 402 SITE 5 AC1 35 MN A 403 MN A 404 HOH A 504 HOH A 506 SITE 6 AC1 35 HOH A 527 HOH A 531 HOH A 537 HOH A 563 SITE 7 AC1 35 HOH A 579 HOH A 590 HOH A 596 HOH A 610 SITE 8 AC1 35 HOH A 624 HOH A 725 HOH A 755 HOH A 761 SITE 9 AC1 35 HOH A 797 HOH A 819 HOH A 845 SITE 1 AC2 5 ATP A 401 HOH A 563 HOH A 624 HOH A 631 SITE 2 AC2 5 HOH A 755 SITE 1 AC3 6 GLU A 123 ATP A 401 HOH A 527 HOH A 531 SITE 2 AC3 6 HOH A 545 HOH A 725 SITE 1 AC4 5 ATP A 401 HOH A 506 HOH A 596 HOH A 797 SITE 2 AC4 5 HOH A 819 CRYST1 53.031 64.221 101.888 90.00 90.00 90.00 P 21 21 21 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 0.018857 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009815 0.00000