HEADER LIGASE 12-FEB-20 6VT9 TITLE NAEGLERIA GRUBERI RNA LIGASE E227A 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 6VT9 1 REMARK REVDAT 3 10-JUN-20 6VT9 1 JRNL REVDAT 2 06-MAY-20 6VT9 1 JRNL REVDAT 1 08-APR-20 6VT9 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. 2.49 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 27618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2785 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 27.5000 - 6.7300 0.98 1243 140 0.1636 0.2455 REMARK 3 2 6.7200 - 5.3600 1.00 1257 144 0.1792 0.2567 REMARK 3 3 5.3500 - 4.6800 1.00 1243 140 0.1596 0.2218 REMARK 3 4 4.6800 - 4.2500 1.00 1274 142 0.1552 0.2589 REMARK 3 5 4.2500 - 3.9500 1.00 1247 141 0.1890 0.2400 REMARK 3 6 3.9500 - 3.7200 0.99 1252 141 0.2376 0.3146 REMARK 3 7 3.7200 - 3.5300 0.99 1233 139 0.2541 0.4436 REMARK 3 8 3.5300 - 3.3800 1.00 1272 147 0.2547 0.3464 REMARK 3 9 3.3800 - 3.2500 1.00 1247 142 0.2539 0.3064 REMARK 3 10 3.2500 - 3.1400 1.00 1260 141 0.2716 0.3564 REMARK 3 11 3.1400 - 3.0400 1.00 1256 143 0.2593 0.3504 REMARK 3 12 3.0400 - 2.9500 1.00 1242 140 0.2641 0.3069 REMARK 3 13 2.9500 - 2.8700 1.00 1267 142 0.2871 0.4241 REMARK 3 14 2.8700 - 2.8000 1.00 1265 136 0.3017 0.3611 REMARK 3 15 2.8000 - 2.7400 1.00 1254 138 0.3130 0.4072 REMARK 3 16 2.7400 - 2.6800 1.00 1277 139 0.3461 0.4477 REMARK 3 17 2.6800 - 2.6300 1.00 1266 141 0.3417 0.4744 REMARK 3 18 2.6300 - 2.5800 1.00 1238 141 0.3485 0.4190 REMARK 3 19 2.5800 - 2.5300 1.00 1268 140 0.3617 0.4306 REMARK 3 20 2.5300 - 2.4900 0.78 972 108 0.3752 0.4645 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) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.51 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 4 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0824 28.1224 24.7000 REMARK 3 T TENSOR REMARK 3 T11: 0.4631 T22: 0.4479 REMARK 3 T33: 0.5508 T12: -0.1011 REMARK 3 T13: -0.0859 T23: 0.0947 REMARK 3 L TENSOR REMARK 3 L11: 6.1236 L22: 4.0691 REMARK 3 L33: 5.8051 L12: 0.2779 REMARK 3 L13: 2.3093 L23: -0.5341 REMARK 3 S TENSOR REMARK 3 S11: -0.1545 S12: -0.1203 S13: 0.0323 REMARK 3 S21: -0.2901 S22: 0.2718 S23: 0.6329 REMARK 3 S31: 0.0714 S32: -0.7904 S33: -0.0580 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 338 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.5191 12.9553 20.9115 REMARK 3 T TENSOR REMARK 3 T11: 0.7700 T22: 0.5754 REMARK 3 T33: 0.7074 T12: 0.0929 REMARK 3 T13: -0.0723 T23: -0.0540 REMARK 3 L TENSOR REMARK 3 L11: 3.5289 L22: 3.7907 REMARK 3 L33: 1.7959 L12: -3.1014 REMARK 3 L13: -1.0188 L23: 2.1812 REMARK 3 S TENSOR REMARK 3 S11: 0.1297 S12: 0.0044 S13: 0.0817 REMARK 3 S21: 0.0913 S22: 0.1897 S23: -0.6102 REMARK 3 S31: 0.3919 S32: 0.4197 S33: -0.3415 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 6VT9 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_1000247044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-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) : 0.9793 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 : 27618 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.70 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 16.60 REMARK 200 R MERGE FOR SHELL (I) : 2.00600 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 (%): 53.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NGRRNLE227A (12 MG/ML) WAS ADJUSTED TO REMARK 280 2 MM ATP AND 5 MM MNCL2 AND INCUBATED FOR 15 MIN ON ICE BEFORE REMARK 280 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 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 52.67350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.21600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.21600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.33675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.21600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.21600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.01025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.21600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.21600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.33675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.21600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.21600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 79.01025 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 52.67350 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 512 LIES ON A SPECIAL POSITION. 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 465 ARG A 339 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 NZ LYS A 326 O1A ATP A 401 2.10 REMARK 500 OG SER A 91 O HOH A 501 2.11 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 OG SER A 131 OE1 GLU A 133 7555 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 34 CB CYS A 34 SG -0.140 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 -70.41 -27.07 REMARK 500 ASP A 53 -8.15 81.82 REMARK 500 TYR A 63 52.48 -119.57 REMARK 500 GLU A 74 25.41 46.16 REMARK 500 GLU A 103 1.40 -67.36 REMARK 500 ASP A 182 -31.79 75.11 REMARK 500 ASP A 183 -0.84 -157.37 REMARK 500 GLN A 234 52.28 39.68 REMARK 500 ASN A 290 46.47 -143.25 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 VAL A 29 ASP A 30 -139.51 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 OD2 REMARK 620 2 ATP A 401 O3G 149.8 REMARK 620 3 ATP A 401 O1B 83.6 71.0 REMARK 620 4 ATP A 401 O2A 84.1 103.6 73.9 REMARK 620 5 HOH A 511 O 87.6 78.1 93.6 165.6 REMARK 620 6 HOH A 515 O 95.9 106.7 171.4 114.7 77.8 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 DBREF 6VT9 A 1 339 UNP D2W2Z5 D2W2Z5_NAEGR 1 339 SEQADV 6VT9 SER A 0 UNP D2W2Z5 EXPRESSION TAG SEQADV 6VT9 ALA A 227 UNP D2W2Z5 GLU 227 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 ALA 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 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 MN MN 2+ FORMUL 4 HOH *15(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 LEU A 153 ASN A 160 1 8 HELIX 5 AA5 ASN A 200 ASN A 209 1 10 HELIX 6 AA6 LYS A 210 ASN A 219 1 10 HELIX 7 AA7 ILE A 233 LEU A 237 5 5 HELIX 8 AA8 THR A 260 ASN A 274 1 15 HELIX 9 AA9 THR A 292 MET A 299 1 8 HELIX 10 AB1 SER A 329 LYS A 335 1 7 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 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 ILE A 134 GLU A 137 0 SHEET 2 AA5 7 TRP A 192 LEU A 194 -1 O GLU A 193 N GLY A 136 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 ILE A 134 GLU A 137 0 SHEET 2 AA6 7 TRP A 192 LEU A 194 -1 O GLU A 193 N GLY A 136 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 5 GLU A 148 ARG A 149 0 SHEET 2 AA7 5 SER A 324 ILE A 328 1 O LYS A 326 N GLU A 148 SHEET 3 AA7 5 GLY A 313 ARG A 318 -1 N PHE A 316 O PHE A 325 SHEET 4 AA7 5 LYS A 164 LYS A 170 -1 N GLU A 166 O LYS A 317 SHEET 5 AA7 5 ILE A 283 GLU A 288 -1 O LEU A 284 N VAL A 167 LINK OD2 ASP A 146 MN MN A 402 1555 1555 1.73 LINK O3G ATP A 401 MN MN A 402 1555 1555 2.23 LINK O1B ATP A 401 MN MN A 402 1555 1555 2.43 LINK O2A ATP A 401 MN MN A 402 1555 1555 2.33 LINK MN MN A 402 O HOH A 511 1555 1555 2.25 LINK MN MN A 402 O HOH A 515 1555 1555 2.60 SITE 1 AC1 19 ARG A 4 LYS A 121 THR A 145 ASP A 146 SITE 2 AC1 19 GLN A 147 ARG A 149 THR A 168 VAL A 169 SITE 3 AC1 19 LYS A 170 LEU A 171 SER A 175 ARG A 190 SITE 4 AC1 19 PHE A 248 VAL A 281 VAL A 315 LYS A 317 SITE 5 AC1 19 LYS A 326 MN A 402 HOH A 511 SITE 1 AC2 5 ASP A 146 ARG A 190 ATP A 401 HOH A 511 SITE 2 AC2 5 HOH A 515 CRYST1 88.432 88.432 105.347 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 0.011308 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009492 0.00000