HEADER LIGASE 04-AUG-15 5D1P TITLE ARCHAEAL ATP-DEPENDENT RNA LIGASE - FORM 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS (STRAIN SOURCE 3 ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H); SOURCE 4 ORGANISM_TAXID: 187420; SOURCE 5 STRAIN: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H; SOURCE 6 GENE: MTH_1221; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ATP-DEPENDENT RNA LIGASE, ARCHAEA, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR K.S.MURAKAMI REVDAT 2 30-MAR-16 5D1P 1 JRNL REVDAT 1 09-MAR-16 5D1P 0 JRNL AUTH H.GU,S.YOSHINARI,R.GHOSH,A.V.IGNATOCHKINA,P.D.GOLLNICK, JRNL AUTH 2 K.S.MURAKAMI,C.K.HO JRNL TITL STRUCTURAL AND MUTATIONAL ANALYSIS OF ARCHAEAL ATP-DEPENDENT JRNL TITL 2 RNA LIGASE IDENTIFIES AMINO ACIDS REQUIRED FOR RNA BINDING JRNL TITL 3 AND CATALYSIS. JRNL REF NUCLEIC ACIDS RES. V. 44 2337 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 26896806 JRNL DOI 10.1093/NAR/GKW094 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 46656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.290 REMARK 3 FREE R VALUE TEST SET COUNT : 2002 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 29.3671 - 5.2899 1.00 3580 160 0.1669 0.2206 REMARK 3 2 5.2899 - 4.2027 1.00 3522 159 0.1500 0.1652 REMARK 3 3 4.2027 - 3.6726 0.99 3511 163 0.1648 0.2201 REMARK 3 4 3.6726 - 3.3373 0.99 3517 155 0.1790 0.2353 REMARK 3 5 3.3373 - 3.0984 0.99 3493 154 0.1960 0.2654 REMARK 3 6 3.0984 - 2.9159 0.99 3475 160 0.2338 0.3070 REMARK 3 7 2.9159 - 2.7700 0.98 3437 160 0.2301 0.2736 REMARK 3 8 2.7700 - 2.6495 0.97 3395 143 0.2321 0.2807 REMARK 3 9 2.6495 - 2.5475 0.94 3307 149 0.2323 0.2890 REMARK 3 10 2.5475 - 2.4597 0.94 3290 149 0.2344 0.2869 REMARK 3 11 2.4597 - 2.3828 0.91 3206 141 0.2275 0.2648 REMARK 3 12 2.3828 - 2.3147 0.79 2795 118 0.2417 0.2784 REMARK 3 13 2.3147 - 2.2538 0.64 2238 101 0.2593 0.3123 REMARK 3 14 2.2538 - 2.1988 0.55 1888 90 0.2898 0.3702 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.210 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 : 0.022 6180 REMARK 3 ANGLE : 1.306 8358 REMARK 3 CHIRALITY : 0.050 892 REMARK 3 PLANARITY : 0.006 1098 REMARK 3 DIHEDRAL : 16.697 2400 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 5D1P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5414 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45957 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 89.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL (PH 8.5), 0.2 M LITHIUM REMARK 280 SULFATE AND 40 % PEG400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 57.65200 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -166.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 4 REMARK 465 ASN A 5 REMARK 465 SER A 6 REMARK 465 MET B 4 REMARK 465 ASN B 5 REMARK 465 SER B 6 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 A 616 O HOH A 773 2.00 REMARK 500 O PHE B 88 O HOH B 601 2.08 REMARK 500 O HOH B 799 O HOH B 807 2.12 REMARK 500 O HOH A 770 O HOH A 782 2.12 REMARK 500 O HOH B 737 O HOH B 773 2.12 REMARK 500 O HOH A 752 O HOH A 763 2.14 REMARK 500 NH1 ARG B 184 O HOH B 602 2.17 REMARK 500 O HOH B 636 O HOH B 784 2.18 REMARK 500 O HOH A 772 O HOH A 776 2.18 REMARK 500 O1 SO4 B 501 O HOH B 603 2.19 REMARK 500 OE1 GLU A 310 O HOH A 601 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 HOH A 744 O HOH A 765 1455 2.13 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 PRO A 270 C - N - CA ANGL. DEV. = -14.3 DEGREES REMARK 500 PRO A 270 C - N - CD ANGL. DEV. = 17.5 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 30 -81.52 -145.48 REMARK 500 SER A 38 131.66 70.61 REMARK 500 ALA A 39 46.99 13.72 REMARK 500 LEU A 50 117.93 -164.22 REMARK 500 ARG A 89 115.26 -160.31 REMARK 500 ASP A 90 -61.93 75.55 REMARK 500 ASP A 156 45.47 -84.44 REMARK 500 ASN A 181 -56.87 71.33 REMARK 500 ARG A 269 -135.76 43.14 REMARK 500 PHE A 271 -77.94 44.86 REMARK 500 ASP A 356 -110.95 56.30 REMARK 500 ARG B 30 -73.21 -122.83 REMARK 500 SER B 32 96.45 52.21 REMARK 500 ALA B 39 -10.60 -158.29 REMARK 500 LEU B 50 106.83 -167.36 REMARK 500 ASP B 90 -64.81 79.94 REMARK 500 TYR B 159 -50.74 -122.75 REMARK 500 ASN B 181 -50.75 75.69 REMARK 500 PHE B 271 88.66 2.98 REMARK 500 PHE B 272 -69.31 166.43 REMARK 500 ASP B 353 145.16 -170.77 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 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 APK A 97 O2P REMARK 620 2 HOH A 648 O 73.6 REMARK 620 3 HOH A 658 O 88.2 79.2 REMARK 620 4 HOH A 694 O 158.7 85.6 83.6 REMARK 620 5 HOH A 622 O 100.1 87.3 161.6 82.8 REMARK 620 6 HOH A 624 O 109.2 174.0 105.9 92.0 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 APK B 97 O2P REMARK 620 2 HOH B 620 O 91.4 REMARK 620 3 HOH B 630 O 99.8 76.2 REMARK 620 4 HOH B 662 O 82.5 83.6 159.7 REMARK 620 5 HOH B 713 O 163.7 76.4 87.9 85.3 REMARK 620 6 HOH B 614 O 95.1 173.0 100.2 99.6 97.7 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 SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D1O RELATED DB: PDB DBREF 5D1P A 4 381 UNP O27289 O27289_METTH 4 381 DBREF 5D1P B 4 381 UNP O27289 O27289_METTH 4 381 SEQRES 1 A 378 MET ASN SER ASP ILE PRO PHE ASP LEU ILE GLN GLU ARG SEQRES 2 A 378 THR GLY VAL PRO SER SER ARG LEU LYS VAL ALA PHE ALA SEQRES 3 A 378 ARG GLY SER LEU ARG LEU LEU GLU SER ALA GLY MET GLN SEQRES 4 A 378 ALA LEU LEU PHE LYS LYS PRO LEU GLY ASP LEU GLU ALA SEQRES 5 A 378 GLY THR VAL ILE TYR LEU GLY ASP GLU THR GLU VAL ILE SEQRES 6 A 378 ARG GLY PHE PRO LYS ILE ARG ARG THR LEU LEU LEU SER SEQRES 7 A 378 PRO THR ILE GLN GLU HIS PHE ARG ASP ARG VAL ALA VAL SEQRES 8 A 378 GLU GLU APK MET ASN GLY TYR ASN VAL ARG ILE ALA CYS SEQRES 9 A 378 LEU SER SER GLY GLU THR VAL ALA LEU THR ARG GLY GLY SEQRES 10 A 378 HIS VAL CYS PRO PHE THR THR ARG LYS ALA GLN GLU LEU SEQRES 11 A 378 LEU ASP LEU SER GLU PHE PHE ARG GLU HIS PRO ASP LEU SEQRES 12 A 378 VAL ILE CYS GLY GLU MET ILE GLY ARG ASP ASN PRO TYR SEQRES 13 A 378 VAL SER GLN ASP TYR PRO GLU VAL GLY PRO LEU GLY PHE SEQRES 14 A 378 ARG VAL PHE ASP LEU ARG GLU LYS ASN THR ASN ARG PRO SEQRES 15 A 378 LEU PRO VAL GLU GLU ARG ARG ALA LEU LEU ASP SER TYR SEQRES 16 A 378 GLY LEU PRO ASN VAL ARG LEU PHE GLY VAL TYR PRO ILE SEQRES 17 A 378 GLU GLU ALA ALA SER GLU VAL ALA ASP ILE ILE ARG ALA SEQRES 18 A 378 LEU GLY MET ALA GLY ARG GLU GLY VAL VAL MET LYS ASP SEQRES 19 A 378 PRO SER MET GLU VAL PRO PRO LEU LYS TYR THR SER SER SEQRES 20 A 378 GLN ALA HIS ALA ARG GLU LEU ALA TYR ALA PHE SER TYR SEQRES 21 A 378 PRO PHE ASP PHE GLY ARG PRO PHE PHE PHE SER ARG VAL SEQRES 22 A 378 ILE ARG GLU GLY PHE GLN ALA TYR GLU LEU ASP GLU SER SEQRES 23 A 378 ASP ASP GLU THR ARG GLU ARG ALA ARG ARG LEU GLY GLU SEQRES 24 A 378 ALA ILE ILE TYR PRO MET LEU GLU ARG ILE LYS SER ILE SEQRES 25 A 378 SER ALA GLY GLU ALA ALA TYR GLU ASP THR VAL ILE ASP SEQRES 26 A 378 VAL GLU ASP ARG GLU ALA ALA GLU GLU PHE ILE ARG HIS SEQRES 27 A 378 LEU VAL ARG LEU GLY VAL SER ALA THR LEU ALA ASP TYR SEQRES 28 A 378 ARG ASP GLY ARG ALA THR ILE ARG ARG PHE TYR GLN SER SEQRES 29 A 378 THR THR ASP ARG ILE ASN ASN TYR LEU LYS GLY GLY LEU SEQRES 30 A 378 TYR SEQRES 1 B 378 MET ASN SER ASP ILE PRO PHE ASP LEU ILE GLN GLU ARG SEQRES 2 B 378 THR GLY VAL PRO SER SER ARG LEU LYS VAL ALA PHE ALA SEQRES 3 B 378 ARG GLY SER LEU ARG LEU LEU GLU SER ALA GLY MET GLN SEQRES 4 B 378 ALA LEU LEU PHE LYS LYS PRO LEU GLY ASP LEU GLU ALA SEQRES 5 B 378 GLY THR VAL ILE TYR LEU GLY ASP GLU THR GLU VAL ILE SEQRES 6 B 378 ARG GLY PHE PRO LYS ILE ARG ARG THR LEU LEU LEU SER SEQRES 7 B 378 PRO THR ILE GLN GLU HIS PHE ARG ASP ARG VAL ALA VAL SEQRES 8 B 378 GLU GLU APK MET ASN GLY TYR ASN VAL ARG ILE ALA CYS SEQRES 9 B 378 LEU SER SER GLY GLU THR VAL ALA LEU THR ARG GLY GLY SEQRES 10 B 378 HIS VAL CYS PRO PHE THR THR ARG LYS ALA GLN GLU LEU SEQRES 11 B 378 LEU ASP LEU SER GLU PHE PHE ARG GLU HIS PRO ASP LEU SEQRES 12 B 378 VAL ILE CYS GLY GLU MET ILE GLY ARG ASP ASN PRO TYR SEQRES 13 B 378 VAL SER GLN ASP TYR PRO GLU VAL GLY PRO LEU GLY PHE SEQRES 14 B 378 ARG VAL PHE ASP LEU ARG GLU LYS ASN THR ASN ARG PRO SEQRES 15 B 378 LEU PRO VAL GLU GLU ARG ARG ALA LEU LEU ASP SER TYR SEQRES 16 B 378 GLY LEU PRO ASN VAL ARG LEU PHE GLY VAL TYR PRO ILE SEQRES 17 B 378 GLU GLU ALA ALA SER GLU VAL ALA ASP ILE ILE ARG ALA SEQRES 18 B 378 LEU GLY MET ALA GLY ARG GLU GLY VAL VAL MET LYS ASP SEQRES 19 B 378 PRO SER MET GLU VAL PRO PRO LEU LYS TYR THR SER SER SEQRES 20 B 378 GLN ALA HIS ALA ARG GLU LEU ALA TYR ALA PHE SER TYR SEQRES 21 B 378 PRO PHE ASP PHE GLY ARG PRO PHE PHE PHE SER ARG VAL SEQRES 22 B 378 ILE ARG GLU GLY PHE GLN ALA TYR GLU LEU ASP GLU SER SEQRES 23 B 378 ASP ASP GLU THR ARG GLU ARG ALA ARG ARG LEU GLY GLU SEQRES 24 B 378 ALA ILE ILE TYR PRO MET LEU GLU ARG ILE LYS SER ILE SEQRES 25 B 378 SER ALA GLY GLU ALA ALA TYR GLU ASP THR VAL ILE ASP SEQRES 26 B 378 VAL GLU ASP ARG GLU ALA ALA GLU GLU PHE ILE ARG HIS SEQRES 27 B 378 LEU VAL ARG LEU GLY VAL SER ALA THR LEU ALA ASP TYR SEQRES 28 B 378 ARG ASP GLY ARG ALA THR ILE ARG ARG PHE TYR GLN SER SEQRES 29 B 378 THR THR ASP ARG ILE ASN ASN TYR LEU LYS GLY GLY LEU SEQRES 30 B 378 TYR MODRES 5D1P APK A 97 LYS MODIFIED RESIDUE MODRES 5D1P APK B 97 LYS MODIFIED RESIDUE HET APK A 97 31 HET APK B 97 31 HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HET MG A 504 1 HET SO4 B 501 5 HET SO4 B 502 5 HET SO4 B 503 5 HET MG B 504 1 HETNAM APK 5'-O-[(S)-{[(5S)-5-AMINO-6-OXOHEXYL]AMINO}(HYDROXY) HETNAM 2 APK PHOSPHORYL]ADENOSINE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION FORMUL 1 APK 2(C16 H26 N7 O7 P) FORMUL 3 SO4 6(O4 S 2-) FORMUL 6 MG 2(MG 2+) FORMUL 11 HOH *404(H2 O) HELIX 1 AA1 PRO A 9 GLY A 18 1 10 HELIX 2 AA2 PRO A 20 ALA A 29 1 10 HELIX 3 AA3 PRO A 82 PHE A 88 1 7 HELIX 4 AA4 CYS A 123 LEU A 134 1 12 HELIX 5 AA5 LEU A 136 HIS A 143 1 8 HELIX 6 AA6 PRO A 187 TYR A 198 1 12 HELIX 7 AA7 ILE A 211 GLY A 229 1 19 HELIX 8 AA8 SER A 249 PHE A 261 1 13 HELIX 9 AA9 PHE A 271 ASP A 287 1 17 HELIX 10 AB1 SER A 289 ALA A 317 1 29 HELIX 11 AB2 ASP A 331 LEU A 345 1 15 HELIX 12 AB3 TYR A 365 LYS A 377 1 13 HELIX 13 AB4 PRO B 9 GLY B 18 1 10 HELIX 14 AB5 PRO B 20 ALA B 29 1 10 HELIX 15 AB6 PRO B 82 PHE B 88 1 7 HELIX 16 AB7 CYS B 123 LEU B 134 1 12 HELIX 17 AB8 LEU B 136 HIS B 143 1 8 HELIX 18 AB9 TYR B 164 GLY B 168 5 5 HELIX 19 AC1 PRO B 187 TYR B 198 1 12 HELIX 20 AC2 ILE B 211 GLY B 229 1 19 HELIX 21 AC3 SER B 249 TYR B 263 1 15 HELIX 22 AC4 PRO B 264 PHE B 267 5 4 HELIX 23 AC5 PHE B 272 ASP B 287 1 16 HELIX 24 AC6 SER B 289 ALA B 317 1 29 HELIX 25 AC7 ASP B 331 LEU B 345 1 15 HELIX 26 AC8 TYR B 365 LYS B 377 1 13 SHEET 1 AA1 4 SER A 32 LEU A 36 0 SHEET 2 AA1 4 GLN A 42 PHE A 46 -1 O LEU A 45 N LEU A 33 SHEET 3 AA1 4 VAL A 58 LEU A 61 -1 O LEU A 61 N GLN A 42 SHEET 4 AA1 4 THR A 65 ILE A 68 -1 O ILE A 68 N VAL A 58 SHEET 1 AA2 5 ARG A 75 ARG A 76 0 SHEET 2 AA2 5 LEU A 245 THR A 248 1 O LYS A 246 N ARG A 75 SHEET 3 AA2 5 GLY A 232 LYS A 236 -1 N MET A 235 O LEU A 245 SHEET 4 AA2 5 ARG A 91 APK A 97 -1 N APK A 97 O GLY A 232 SHEET 5 AA2 5 LEU A 205 PRO A 210 -1 O PHE A 206 N VAL A 94 SHEET 1 AA3 4 THR A 113 LEU A 116 0 SHEET 2 AA3 4 TYR A 101 CYS A 107 -1 N ARG A 104 O LEU A 116 SHEET 3 AA3 4 LEU A 146 ILE A 153 -1 O MET A 152 N TYR A 101 SHEET 4 AA3 4 GLY A 171 GLU A 179 -1 O ARG A 178 N VAL A 147 SHEET 1 AA4 3 TYR A 322 ASP A 328 0 SHEET 2 AA4 3 ARG A 358 PHE A 364 -1 O ARG A 363 N GLU A 323 SHEET 3 AA4 3 ALA A 349 ARG A 355 -1 N ARG A 355 O ARG A 358 SHEET 1 AA5 4 LEU B 33 LEU B 36 0 SHEET 2 AA5 4 GLN B 42 LEU B 45 -1 O ALA B 43 N LEU B 35 SHEET 3 AA5 4 VAL B 58 LEU B 61 -1 O ILE B 59 N LEU B 44 SHEET 4 AA5 4 THR B 65 ILE B 68 -1 O GLU B 66 N TYR B 60 SHEET 1 AA6 5 ARG B 75 ARG B 76 0 SHEET 2 AA6 5 LEU B 245 THR B 248 1 O LYS B 246 N ARG B 75 SHEET 3 AA6 5 GLY B 232 LYS B 236 -1 N MET B 235 O LEU B 245 SHEET 4 AA6 5 ARG B 91 APK B 97 -1 N ALA B 93 O LYS B 236 SHEET 5 AA6 5 LEU B 205 PRO B 210 -1 O TYR B 209 N VAL B 92 SHEET 1 AA7 4 THR B 113 LEU B 116 0 SHEET 2 AA7 4 TYR B 101 CYS B 107 -1 N ARG B 104 O LEU B 116 SHEET 3 AA7 4 LEU B 146 ILE B 153 -1 O MET B 152 N TYR B 101 SHEET 4 AA7 4 GLY B 171 GLU B 179 -1 O ARG B 178 N VAL B 147 SHEET 1 AA8 3 TYR B 322 ASP B 328 0 SHEET 2 AA8 3 ARG B 358 PHE B 364 -1 O ARG B 363 N GLU B 323 SHEET 3 AA8 3 ALA B 349 ARG B 355 -1 N ASP B 353 O THR B 360 LINK C GLU A 96 N APK A 97 1555 1555 1.33 LINK C APK A 97 N MET A 98 1555 1555 1.33 LINK O2P APK A 97 MG MG A 504 1555 1555 2.26 LINK C GLU B 96 N APK B 97 1555 1555 1.34 LINK C APK B 97 N MET B 98 1555 1555 1.33 LINK O2P APK B 97 MG MG B 504 1555 1555 2.04 LINK MG MG A 504 O HOH A 648 1555 1555 2.05 LINK MG MG A 504 O HOH A 658 1555 1555 2.32 LINK MG MG A 504 O HOH A 694 1555 1555 2.21 LINK MG MG A 504 O HOH A 622 1555 1555 2.24 LINK MG MG A 504 O HOH A 624 1555 1555 2.19 LINK MG MG B 504 O HOH B 620 1555 1555 2.21 LINK MG MG B 504 O HOH B 630 1555 1555 2.32 LINK MG MG B 504 O HOH B 662 1555 1555 2.05 LINK MG MG B 504 O HOH B 713 1555 1555 1.98 LINK MG MG B 504 O HOH B 614 1555 1555 2.04 CISPEP 1 SER A 81 PRO A 82 0 4.14 CISPEP 2 PRO A 270 PHE A 271 0 -3.04 CISPEP 3 GLY B 31 SER B 32 0 -27.92 CISPEP 4 SER B 38 ALA B 39 0 -3.00 CISPEP 5 SER B 81 PRO B 82 0 1.62 CISPEP 6 GLY B 268 ARG B 269 0 7.49 CISPEP 7 PRO B 270 PHE B 271 0 -7.29 SITE 1 AC1 8 ARG A 76 APK A 97 LYS A 246 ARG A 278 SITE 2 AC1 8 SO4 A 502 HOH A 635 HOH A 690 HOH A 697 SITE 1 AC2 8 LYS A 73 ILE A 74 APK A 97 ARG A 118 SITE 2 AC2 8 LYS A 246 SO4 A 501 HOH A 656 HOH A 660 SITE 1 AC3 8 PRO A 20 ARG A 23 GLN A 251 ARG A 298 SITE 2 AC3 8 ARG A 299 HOH A 663 HOH A 700 HOH A 703 SITE 1 AC4 6 APK A 97 HOH A 622 HOH A 624 HOH A 648 SITE 2 AC4 6 HOH A 658 HOH A 694 SITE 1 AC5 8 ARG B 76 APK B 97 LYS B 246 ARG B 278 SITE 2 AC5 8 SO4 B 502 HOH B 603 HOH B 665 HOH B 727 SITE 1 AC6 8 LYS B 73 ILE B 74 APK B 97 ARG B 118 SITE 2 AC6 8 LYS B 246 SO4 B 501 HOH B 634 HOH B 659 SITE 1 AC7 2 ASP B 163 ARG B 255 SITE 1 AC8 6 APK B 97 HOH B 614 HOH B 620 HOH B 630 SITE 2 AC8 6 HOH B 662 HOH B 713 CRYST1 50.500 115.304 91.567 90.00 104.55 90.00 P 1 21 1 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 0.019802 0.000000 0.005140 0.00000 SCALE2 0.000000 0.008673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011283 0.00000