HEADER TRANSLATION 24-NOV-17 5YV5 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF ARCHAEAL RIBOSOMAL STALK PROTEIN TITLE 2 AP1 AND ARCHAEAL RIBOSOME RECYCLING FACTOR AABCE1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE RIL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ARCHAEAL RIBOSOMAL STALK PROTEIN AP1; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS COM1; SOURCE 3 ORGANISM_TAXID: 1185654; SOURCE 4 GENE: PFC_02505; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 10 ORGANISM_TAXID: 2261 KEYWDS RIBOSOME RECYCLING, RIBOSOMAL STALK, COMPLEX, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR H.IMAI,T.ABE,T.MIYOSHI,S.NISHIKAWA,K.ITO,T.UCHIUMI REVDAT 5 13-NOV-24 5YV5 1 REMARK REVDAT 4 22-NOV-23 5YV5 1 LINK REVDAT 3 19-SEP-18 5YV5 1 JRNL REVDAT 2 01-AUG-18 5YV5 1 JRNL REVDAT 1 18-JUL-18 5YV5 0 JRNL AUTH H.IMAI,T.ABE,T.MIYOSHI,S.I.NISHIKAWA,K.ITO,T.UCHIUMI JRNL TITL THE RIBOSOMAL STALK PROTEIN IS CRUCIAL FOR THE ACTION OF THE JRNL TITL 2 CONSERVED ATPASE ABCE1 JRNL REF NUCLEIC ACIDS RES. V. 46 7820 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30010948 JRNL DOI 10.1093/NAR/GKY619 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 31682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1714 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1851 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4199 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 292 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.243 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.199 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.942 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4332 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4140 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5860 ; 1.104 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9579 ; 0.713 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 529 ; 5.508 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;34.005 ;23.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 774 ;13.500 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.372 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 647 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4772 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 878 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2122 ; 1.157 ; 2.853 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2121 ; 1.157 ; 2.851 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2649 ; 2.016 ; 4.269 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2650 ; 2.015 ; 4.271 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2210 ; 1.276 ; 3.014 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2210 ; 1.276 ; 3.014 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3211 ; 2.212 ; 4.440 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4866 ; 4.130 ;33.226 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4806 ; 4.023 ;33.051 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-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) : 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31682 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.180 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 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: BALBES REMARK 200 STARTING MODEL: 1YQT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% (W/V) PEG 4000, 10% (V/V) 2 REMARK 280 -PROPANOL, 0.1 M HEPES PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 30.00550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.53650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.36550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.53650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.00550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.36550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 55 REMARK 465 GLY A 56 REMARK 465 SER A 57 REMARK 465 SER A 58 REMARK 465 HIS A 59 REMARK 465 HIS A 60 REMARK 465 HIS A 61 REMARK 465 HIS A 62 REMARK 465 HIS A 63 REMARK 465 HIS A 64 REMARK 465 SER A 65 REMARK 465 SER A 66 REMARK 465 GLY A 67 REMARK 465 LEU A 68 REMARK 465 VAL A 69 REMARK 465 PRO A 70 REMARK 465 ARG A 71 REMARK 465 GLY A 72 REMARK 465 ALA A 590 REMARK 465 GLU B 91 REMARK 465 GLU B 92 REMARK 465 GLU B 93 REMARK 465 VAL B 94 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 95 OG REMARK 470 GLU B 96 CG CD OE1 OE2 REMARK 470 GLU B 97 CG CD OE1 OE2 REMARK 470 GLU B 98 CG CD OE1 OE2 REMARK 470 LEU B 100 CG CD1 CD2 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 ASN A 86 -51.88 169.56 REMARK 500 ARG A 92 167.53 70.02 REMARK 500 ARG A 159 85.70 -151.80 REMARK 500 TYR A 240 -2.89 75.45 REMARK 500 ASP A 398 68.88 -116.71 REMARK 500 LEU A 437 -61.36 -122.79 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 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 113 OG REMARK 620 2 GLN A 165 OE1 86.7 REMARK 620 3 ADP A 601 O3B 94.4 174.1 REMARK 620 4 HOH A 720 O 88.5 90.8 83.4 REMARK 620 5 HOH A 721 O 92.3 86.7 99.0 177.4 REMARK 620 6 HOH A 826 O 174.4 87.8 91.2 92.5 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 378 OG1 REMARK 620 2 GLN A 406 OE1 81.4 REMARK 620 3 ADP A 602 O1B 90.9 172.3 REMARK 620 4 HOH A 728 O 89.6 93.1 86.0 REMARK 620 5 HOH A 744 O 87.3 82.9 97.6 175.3 REMARK 620 6 HOH A 821 O 172.8 93.2 94.5 95.5 87.3 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 ADP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 604 DBREF 5YV5 A 75 590 UNP I6V0C7 I6V0C7_9EURY 75 590 DBREF 5YV5 B 91 108 PDB 5YV5 5YV5 91 108 SEQADV 5YV5 MET A 55 UNP I6V0C7 INITIATING METHIONINE SEQADV 5YV5 GLY A 56 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 SER A 57 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 SER A 58 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 HIS A 59 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 HIS A 60 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 HIS A 61 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 HIS A 62 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 HIS A 63 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 HIS A 64 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 SER A 65 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 SER A 66 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 GLY A 67 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 LEU A 68 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 VAL A 69 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 PRO A 70 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 ARG A 71 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 GLY A 72 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 SER A 73 UNP I6V0C7 EXPRESSION TAG SEQADV 5YV5 HIS A 74 UNP I6V0C7 EXPRESSION TAG SEQRES 1 A 536 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 536 LEU VAL PRO ARG GLY SER HIS LEU GLU GLU ASP CYS VAL SEQRES 3 A 536 HIS ARG TYR GLY VAL ASN ALA PHE VAL LEU TYR ARG LEU SEQRES 4 A 536 PRO VAL VAL LYS GLU GLY MET VAL VAL GLY ILE VAL GLY SEQRES 5 A 536 PRO ASN GLY THR GLY LYS SER THR ALA VAL LYS ILE LEU SEQRES 6 A 536 ALA GLY GLN LEU ILE PRO ASN LEU CYS GLY ASP ASN ASP SEQRES 7 A 536 SER TRP ASP GLY VAL ILE ARG ALA PHE ARG GLY ASN GLU SEQRES 8 A 536 LEU GLN ASN TYR PHE GLU LYS LEU LYS ASN GLY GLU ILE SEQRES 9 A 536 ARG PRO VAL VAL LYS PRO GLN TYR VAL ASP LEU ILE PRO SEQRES 10 A 536 LYS ALA VAL LYS GLY LYS VAL ILE GLU LEU LEU LYS LYS SEQRES 11 A 536 ALA ASP GLU THR GLY LYS LEU GLU GLU VAL VAL LYS ALA SEQRES 12 A 536 LEU GLU LEU GLU ASN VAL LEU ASP ARG GLU ILE GLN HIS SEQRES 13 A 536 LEU SER GLY GLY GLU LEU GLN ARG VAL ALA ILE ALA ALA SEQRES 14 A 536 ALA LEU LEU ARG ASN ALA THR PHE TYR PHE PHE ASP GLU SEQRES 15 A 536 PRO SER SER TYR LEU ASP ILE ARG GLN ARG LEU ASN ALA SEQRES 16 A 536 ALA ARG ALA ILE ARG ARG LEU SER GLU GLU GLY LYS SER SEQRES 17 A 536 VAL LEU VAL VAL GLU HIS ASP LEU ALA VAL LEU ASP TYR SEQRES 18 A 536 LEU SER ASP ILE ILE HIS VAL VAL TYR GLY GLU PRO GLY SEQRES 19 A 536 VAL TYR GLY ILE PHE SER GLN PRO LYS GLY THR ARG ASN SEQRES 20 A 536 GLY ILE ASN GLU PHE LEU ARG GLY TYR LEU LYS ASP GLU SEQRES 21 A 536 ASN VAL ARG PHE ARG PRO TYR GLU ILE LYS PHE THR LYS SEQRES 22 A 536 THR GLY GLU ARG VAL GLU ILE GLU ARG GLU THR LEU VAL SEQRES 23 A 536 THR TYR PRO ARG LEU VAL LYS ASP TYR GLY SER PHE ARG SEQRES 24 A 536 LEU GLU VAL GLU PRO GLY GLU ILE LYS LYS GLY GLU VAL SEQRES 25 A 536 ILE GLY ILE VAL GLY PRO ASN GLY ILE GLY LYS THR THR SEQRES 26 A 536 PHE VAL LYS MET LEU ALA GLY VAL GLU GLU PRO THR GLU SEQRES 27 A 536 GLY LYS ILE GLU TRP ASP LEU THR VAL ALA TYR LYS PRO SEQRES 28 A 536 GLN TYR ILE LYS ALA ASP TYR GLU GLY THR VAL TYR GLU SEQRES 29 A 536 LEU LEU SER LYS ILE ASP ALA SER LYS LEU ASN SER ASN SEQRES 30 A 536 PHE TYR LYS THR GLU LEU LEU LYS PRO LEU GLY ILE ILE SEQRES 31 A 536 ASP LEU TYR ASP ARG GLU VAL ASN GLU LEU SER GLY GLY SEQRES 32 A 536 GLU LEU GLN ARG VAL ALA ILE ALA ALA THR LEU LEU ARG SEQRES 33 A 536 ASP ALA ASP ILE TYR LEU LEU ASP GLU PRO SER ALA TYR SEQRES 34 A 536 LEU ASP VAL GLU GLN ARG LEU ALA VAL SER ARG ALA ILE SEQRES 35 A 536 ARG HIS LEU MET GLU LYS ASN GLU LYS THR ALA LEU VAL SEQRES 36 A 536 VAL GLU HIS ASP VAL LEU MET ILE ASP TYR VAL SER ASP SEQRES 37 A 536 ARG LEU MET VAL PHE GLU GLY GLU PRO GLY LYS TYR GLY SEQRES 38 A 536 ARG ALA LEU PRO PRO MET GLY MET ARG GLU GLY MET ASN SEQRES 39 A 536 ARG PHE LEU ALA SER ILE GLY ILE THR PHE ARG ARG ASP SEQRES 40 A 536 PRO ASP THR GLY ARG PRO ARG ALA ASN LYS GLU GLY SER SEQRES 41 A 536 VAL LYS ASP ARG GLU GLN LYS GLU LYS GLY GLU TYR TYR SEQRES 42 A 536 TYR ILE ALA SEQRES 1 B 18 GLU GLU GLU VAL SER GLU GLU GLU ALA LEU ALA GLY LEU SEQRES 2 B 18 SER ALA LEU PHE GLY HET ADP A 601 27 HET ADP A 602 27 HET MG A 603 1 HET MG A 604 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *292(H2 O) HELIX 1 AA1 GLY A 111 ALA A 120 1 10 HELIX 2 AA2 SER A 133 PHE A 141 1 9 HELIX 3 AA3 GLU A 145 ASN A 155 1 11 HELIX 4 AA4 TYR A 166 ASP A 168 5 3 HELIX 5 AA5 LEU A 169 VAL A 174 1 6 HELIX 6 AA6 LYS A 177 ASP A 186 1 10 HELIX 7 AA7 LYS A 190 LEU A 198 1 9 HELIX 8 AA8 GLU A 207 LEU A 211 5 5 HELIX 9 AA9 SER A 212 ARG A 227 1 16 HELIX 10 AB1 ASP A 242 GLU A 259 1 18 HELIX 11 AB2 ASP A 269 SER A 277 1 9 HELIX 12 AB3 THR A 299 GLY A 309 1 11 HELIX 13 AB4 GLY A 376 ALA A 385 1 10 HELIX 14 AB5 THR A 415 ASN A 429 1 15 HELIX 15 AB6 SER A 430 LEU A 437 1 8 HELIX 16 AB7 ILE A 443 TYR A 447 5 5 HELIX 17 AB8 GLU A 450 LEU A 454 5 5 HELIX 18 AB9 SER A 455 ARG A 470 1 16 HELIX 19 AC1 ASP A 485 GLU A 504 1 20 HELIX 20 AC2 ASP A 513 SER A 521 1 9 HELIX 21 AC3 MET A 543 SER A 553 1 11 HELIX 22 AC4 SER A 574 GLY A 584 1 11 HELIX 23 AC5 GLU B 96 GLY B 108 1 13 SHEET 1 AA1 8 CYS A 79 ARG A 82 0 SHEET 2 AA1 8 VAL A 89 TYR A 91 -1 O LEU A 90 N HIS A 81 SHEET 3 AA1 8 TYR A 290 PHE A 293 1 O GLY A 291 N TYR A 91 SHEET 4 AA1 8 ILE A 279 GLU A 286 -1 N TYR A 284 O ILE A 292 SHEET 5 AA1 8 VAL A 101 VAL A 105 1 N GLY A 103 O ILE A 279 SHEET 6 AA1 8 SER A 262 VAL A 266 1 O VAL A 263 N VAL A 102 SHEET 7 AA1 8 PHE A 231 ASP A 235 1 N PHE A 234 O LEU A 264 SHEET 8 AA1 8 VAL A 161 LYS A 163 1 N VAL A 161 O PHE A 233 SHEET 1 AA2 5 CYS A 79 ARG A 82 0 SHEET 2 AA2 5 VAL A 89 TYR A 91 -1 O LEU A 90 N HIS A 81 SHEET 3 AA2 5 TYR A 290 PHE A 293 1 O GLY A 291 N TYR A 91 SHEET 4 AA2 5 ILE A 279 GLU A 286 -1 N TYR A 284 O ILE A 292 SHEET 5 AA2 5 LYS A 297 GLY A 298 -1 O LYS A 297 N ILE A 280 SHEET 1 AA3 2 TYR A 310 LEU A 311 0 SHEET 2 AA3 2 VAL A 316 ARG A 317 -1 O VAL A 316 N LEU A 311 SHEET 1 AA4 2 THR A 338 TYR A 342 0 SHEET 2 AA4 2 GLY A 359 LYS A 362 -1 O ILE A 361 N VAL A 340 SHEET 1 AA5 8 LEU A 345 TYR A 349 0 SHEET 2 AA5 8 PHE A 352 VAL A 356 -1 O VAL A 356 N LEU A 345 SHEET 3 AA5 8 TYR A 534 ALA A 537 1 O GLY A 535 N GLU A 355 SHEET 4 AA5 8 ARG A 523 GLU A 530 -1 N GLU A 528 O ARG A 536 SHEET 5 AA5 8 VAL A 366 VAL A 370 1 N GLY A 368 O MET A 525 SHEET 6 AA5 8 THR A 506 VAL A 510 1 O VAL A 509 N ILE A 369 SHEET 7 AA5 8 ILE A 474 ASP A 478 1 N LEU A 477 O LEU A 508 SHEET 8 AA5 8 VAL A 401 LYS A 404 1 N LYS A 404 O LEU A 476 SHEET 1 AA6 5 LEU A 345 TYR A 349 0 SHEET 2 AA6 5 PHE A 352 VAL A 356 -1 O VAL A 356 N LEU A 345 SHEET 3 AA6 5 TYR A 534 ALA A 537 1 O GLY A 535 N GLU A 355 SHEET 4 AA6 5 ARG A 523 GLU A 530 -1 N GLU A 528 O ARG A 536 SHEET 5 AA6 5 MET A 541 GLY A 542 -1 O MET A 541 N LEU A 524 SHEET 1 AA7 2 PHE A 558 ARG A 560 0 SHEET 2 AA7 2 PRO A 567 ALA A 569 -1 O ARG A 568 N ARG A 559 SSBOND 1 CYS A 79 CYS A 128 1555 1555 2.03 LINK OG SER A 113 MG MG A 603 1555 1555 2.06 LINK OE1 GLN A 165 MG MG A 603 1555 1555 2.08 LINK OG1 THR A 378 MG MG A 604 1555 1555 2.11 LINK OE1 GLN A 406 MG MG A 604 1555 1555 2.07 LINK O3B ADP A 601 MG MG A 603 1555 1555 2.04 LINK O1B ADP A 602 MG MG A 604 1555 1555 2.05 LINK MG MG A 603 O HOH A 720 1555 1555 2.20 LINK MG MG A 603 O HOH A 721 1555 1555 2.05 LINK MG MG A 603 O HOH A 826 1555 1555 2.09 LINK MG MG A 604 O HOH A 728 1555 1555 2.01 LINK MG MG A 604 O HOH A 744 1555 1555 2.20 LINK MG MG A 604 O HOH A 821 1555 1555 2.04 SITE 1 AC1 15 TYR A 83 ASN A 86 PHE A 88 ASN A 108 SITE 2 AC1 15 GLY A 109 THR A 110 GLY A 111 LYS A 112 SITE 3 AC1 15 SER A 113 THR A 114 GLY A 288 MG A 603 SITE 4 AC1 15 HOH A 720 HOH A 725 HOH A 826 SITE 1 AC2 23 TYR A 349 PHE A 352 ASN A 373 GLY A 374 SITE 2 AC2 23 ILE A 375 GLY A 376 LYS A 377 THR A 378 SITE 3 AC2 23 THR A 379 TYR A 417 TYR A 447 GLY A 532 SITE 4 AC2 23 MG A 604 HOH A 713 HOH A 715 HOH A 728 SITE 5 AC2 23 HOH A 777 HOH A 796 HOH A 821 HOH A 867 SITE 6 AC2 23 HOH A 872 HOH A 893 HOH A 909 SITE 1 AC3 7 SER A 113 GLN A 165 GLU A 236 ADP A 601 SITE 2 AC3 7 HOH A 720 HOH A 721 HOH A 826 SITE 1 AC4 7 THR A 378 GLN A 406 GLU A 479 ADP A 602 SITE 2 AC4 7 HOH A 728 HOH A 744 HOH A 821 CRYST1 60.011 64.731 147.073 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 0.016664 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015449 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006799 0.00000