HEADER LIGASE 12-FEB-20 6VTD TITLE NAEGLERIA GRUBERI RNA LIGASE R149A 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 6VTD 1 LINK REVDAT 3 10-JUN-20 6VTD 1 JRNL REVDAT 2 06-MAY-20 6VTD 1 JRNL REVDAT 1 08-APR-20 6VTD 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. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 29868 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2977 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 27.0500 - 6.6000 0.97 1267 129 0.1797 0.2440 REMARK 3 2 6.6000 - 5.2600 0.99 1263 143 0.1996 0.3178 REMARK 3 3 5.2500 - 4.5900 0.99 1277 142 0.1868 0.2413 REMARK 3 4 4.5900 - 4.1700 0.99 1279 142 0.1892 0.2571 REMARK 3 5 4.1700 - 3.8700 1.00 1280 141 0.2250 0.2974 REMARK 3 6 3.8700 - 3.6500 1.00 1282 143 0.2489 0.2889 REMARK 3 7 3.6500 - 3.4600 0.99 1296 141 0.2473 0.3106 REMARK 3 8 3.4600 - 3.3100 1.00 1265 143 0.2775 0.3388 REMARK 3 9 3.3100 - 3.1900 1.00 1282 144 0.3017 0.3314 REMARK 3 10 3.1900 - 3.0800 1.00 1279 146 0.2925 0.3469 REMARK 3 11 3.0800 - 2.9800 1.00 1271 138 0.3068 0.3763 REMARK 3 12 2.9800 - 2.8900 1.00 1311 144 0.2993 0.2806 REMARK 3 13 2.8900 - 2.8200 1.00 1283 143 0.3041 0.4285 REMARK 3 14 2.8200 - 2.7500 1.00 1261 140 0.3223 0.3102 REMARK 3 15 2.7500 - 2.6900 1.00 1274 141 0.3507 0.3800 REMARK 3 16 2.6900 - 2.6300 1.00 1316 146 0.3286 0.3248 REMARK 3 17 2.6300 - 2.5800 1.00 1281 146 0.3515 0.4304 REMARK 3 18 2.5800 - 2.5300 1.00 1268 141 0.3412 0.4171 REMARK 3 19 2.5300 - 2.4800 1.00 1300 143 0.3561 0.3823 REMARK 3 20 2.4800 - 2.4400 1.00 1283 137 0.3597 0.4339 REMARK 3 21 2.4400 - 2.4000 1.00 1273 144 0.3652 0.4041 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.29 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 : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.4667 28.0116 24.2411 REMARK 3 T TENSOR REMARK 3 T11: 0.3539 T22: 0.4023 REMARK 3 T33: 0.4382 T12: -0.0896 REMARK 3 T13: -0.0720 T23: 0.0611 REMARK 3 L TENSOR REMARK 3 L11: 6.7905 L22: 3.9838 REMARK 3 L33: 6.0216 L12: 0.3822 REMARK 3 L13: 0.0478 L23: -0.9645 REMARK 3 S TENSOR REMARK 3 S11: -0.1652 S12: -0.1850 S13: 0.0465 REMARK 3 S21: -0.2017 S22: 0.3469 S23: 0.4489 REMARK 3 S31: 0.3058 S32: -0.8724 S33: -0.1128 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4810 13.2412 15.1702 REMARK 3 T TENSOR REMARK 3 T11: 0.7641 T22: 0.5418 REMARK 3 T33: 0.5567 T12: 0.1592 REMARK 3 T13: 0.0020 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 4.0379 L22: 3.1329 REMARK 3 L33: 1.3036 L12: -2.1158 REMARK 3 L13: -0.6802 L23: 1.6651 REMARK 3 S TENSOR REMARK 3 S11: 0.2736 S12: 0.6943 S13: -0.2237 REMARK 3 S21: -0.4089 S22: -0.2694 S23: -0.3223 REMARK 3 S31: 0.4992 S32: 0.1268 S33: 0.0127 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 201 THROUGH 339 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.7529 13.1751 23.0832 REMARK 3 T TENSOR REMARK 3 T11: 0.7100 T22: 0.5423 REMARK 3 T33: 0.4778 T12: 0.2483 REMARK 3 T13: -0.0402 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 2.8872 L22: 4.4231 REMARK 3 L33: 1.6104 L12: -1.3803 REMARK 3 L13: -0.1245 L23: 2.9189 REMARK 3 S TENSOR REMARK 3 S11: 0.1065 S12: 0.2095 S13: -0.1716 REMARK 3 S21: -0.1306 S22: 0.2318 S23: -0.5561 REMARK 3 S31: 0.5443 S32: 0.4263 S33: -0.3132 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 6VTD 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_1000247050. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-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 : 29868 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 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 (%): 52.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NGRRNLR149A (8.2 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, 27% PEG6000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 50.46300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.38750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.38750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.23150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.38750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.38750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.69450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.38750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.38750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.23150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.38750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.38750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.69450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.46300 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 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 SER A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 VAL A 3 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 OD2 ASP A 244 NZ LYS A 279 1.96 REMARK 500 OD1 ASP A 53 O HOH A 501 2.14 REMARK 500 OE1 GLN A 76 O HOH A 502 2.18 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 LYS A 5 57.26 -118.64 REMARK 500 ASP A 30 -126.69 53.76 REMARK 500 ASP A 59 114.04 -161.55 REMARK 500 ASP A 182 -112.95 60.48 REMARK 500 SER A 232 -16.04 70.71 REMARK 500 ASN A 290 10.82 -168.42 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 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 146 OD1 REMARK 620 2 ATP A 401 O2A 106.8 REMARK 620 N 1 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 ASP A 172 OD1 REMARK 620 2 ATP A 401 O1G 161.2 REMARK 620 3 ATP A 401 O2G 126.5 55.3 REMARK 620 4 HOH A 512 O 92.7 68.8 96.0 REMARK 620 5 HOH A 520 O 118.0 80.8 69.8 149.1 REMARK 620 N 1 2 3 4 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 O3G REMARK 620 2 ATP A 401 O1B 75.2 REMARK 620 N 1 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 6VTD A 1 339 UNP D2W2Z5 D2W2Z5_NAEGR 1 339 SEQADV 6VTD SER A 0 UNP D2W2Z5 EXPRESSION TAG SEQADV 6VTD ALA A 149 UNP D2W2Z5 ARG 149 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 ALA 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 LYS 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 *50(H2 O) HELIX 1 AA1 TYR A 63 LYS A 68 5 6 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 ALA 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 ALA A 298 1 7 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 VAL A 70 ASP A 72 0 SHEET 2 AA3 4 ARG A 77 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 ILE A 134 GLU A 137 0 SHEET 2 AA5 7 TRP A 192 LEU A 194 -1 O GLU A 193 N LEU A 135 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 LYS A 181 O HIS A 184 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 TYR A 246 N GLU A 227 SHEET 7 AA5 7 GLN A 257 TYR A 258 -1 O GLN A 257 N ASP A 252 SHEET 1 AA6 7 ILE A 134 GLU A 137 0 SHEET 2 AA6 7 TRP A 192 LEU A 194 -1 O GLU A 193 N LEU A 135 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 LYS A 181 O HIS A 184 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 TYR A 246 N GLU A 227 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 OD1 ASP A 146 MN MN A 402 1555 1555 2.64 LINK OD1 ASP A 172 MN MN A 403 1555 1555 2.79 LINK O2A ATP A 401 MN MN A 402 1555 1555 2.23 LINK O1G ATP A 401 MN MN A 403 1555 1555 2.75 LINK O2G ATP A 401 MN MN A 403 1555 1555 2.71 LINK O3G ATP A 401 MN MN A 404 1555 1555 2.24 LINK O1B ATP A 401 MN MN A 404 1555 1555 2.41 LINK MN MN A 403 O HOH A 512 1555 1555 2.47 LINK MN MN A 403 O HOH A 520 1555 1555 2.51 SITE 1 AC1 21 LYS A 121 THR A 145 ASP A 146 GLN A 147 SITE 2 AC1 21 THR A 168 VAL A 169 LYS A 170 LEU A 171 SITE 3 AC1 21 SER A 175 ARG A 190 GLU A 227 PHE A 248 SITE 4 AC1 21 VAL A 281 VAL A 315 LYS A 317 LYS A 326 SITE 5 AC1 21 MN A 402 MN A 403 MN A 404 HOH A 512 SITE 6 AC1 21 HOH A 520 SITE 1 AC2 2 ASP A 146 ATP A 401 SITE 1 AC3 4 ASP A 172 ATP A 401 HOH A 512 HOH A 520 SITE 1 AC4 1 ATP A 401 CRYST1 88.775 88.775 100.926 90.00 90.00 90.00 P 41 21 2 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 0.011264 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009908 0.00000