HEADER VIRAL PROTEIN 07-MAY-18 5ZUA TITLE CRYSTAL STRUCTURE OF MERS-COV MACRO DOMAIN IN COMPLEX WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MACRO DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MIDDLE EAST RESPIRATORY SYNDROME-RELATED SOURCE 3 CORONAVIRUS; SOURCE 4 ORGANISM_TAXID: 1335626; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LIGAND, COMPLEX, MACRO DOMAIN, ATP, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.-H.LIN,C.-C.CHO,C.-Y.CHIEN,C.-H.HSU REVDAT 2 22-NOV-23 5ZUA 1 REMARK REVDAT 1 05-JUN-19 5ZUA 0 JRNL AUTH M.-H.LIN,C.-C.CHO,C.-Y.CHIEN,C.-H.HSU JRNL TITL CRYSTAL STRUCTURE OF MERS-COV MACRO DOMAIN IN COMPLEX WITH JRNL TITL 2 ATP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 4566 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 456 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 28.0339 - 3.5625 0.94 1477 163 0.1512 0.2108 REMARK 3 2 3.5625 - 2.8285 0.89 1362 152 0.1869 0.2645 REMARK 3 3 2.8285 - 2.4712 0.84 1271 141 0.2008 0.2517 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.040 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 : 0.008 1291 REMARK 3 ANGLE : 0.923 1760 REMARK 3 CHIRALITY : 0.057 212 REMARK 3 PLANARITY : 0.005 217 REMARK 3 DIHEDRAL : 13.818 763 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 5ZUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97622 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4573 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.471 REMARK 200 RESOLUTION RANGE LOW (A) : 28.032 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4780 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 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 : 3.685 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5DUS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM CITRATE, 0.1M HEPES SODIUM REMARK 280 PH7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K 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 19.55650 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 GLY A -3 REMARK 465 SER A -2 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 O2A ATP A 201 O HOH A 301 1.97 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 SER A 85 16.13 55.88 REMARK 500 REMARK 500 REMARK: NULL 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 201 DBREF 5ZUA A 1 164 UNP T2B9G2 T2B9G2_9BETC 1110 1273 SEQADV 5ZUA GLY A -3 UNP T2B9G2 EXPRESSION TAG SEQADV 5ZUA SER A -2 UNP T2B9G2 EXPRESSION TAG SEQADV 5ZUA HIS A -1 UNP T2B9G2 EXPRESSION TAG SEQADV 5ZUA MET A 0 UNP T2B9G2 EXPRESSION TAG SEQRES 1 A 168 GLY SER HIS MET PRO LEU SER ASN PHE GLU HIS LYS VAL SEQRES 2 A 168 ILE THR GLU CYS VAL THR ILE VAL LEU GLY ASP ALA ILE SEQRES 3 A 168 GLN VAL ALA LYS CYS TYR GLY GLU SER VAL LEU VAL ASN SEQRES 4 A 168 ALA ALA ASN THR HIS LEU LYS HIS GLY GLY GLY ILE ALA SEQRES 5 A 168 GLY ALA ILE ASN ALA ALA SER LYS GLY ALA VAL GLN LYS SEQRES 6 A 168 GLU SER ASP GLU TYR ILE LEU ALA LYS GLY PRO LEU GLN SEQRES 7 A 168 VAL GLY ASP SER VAL LEU LEU GLN GLY HIS SER LEU ALA SEQRES 8 A 168 LYS ASN ILE LEU HIS VAL VAL GLY PRO ASP ALA ARG ALA SEQRES 9 A 168 LYS GLN ASP VAL SER LEU LEU SER LYS CYS TYR LYS ALA SEQRES 10 A 168 MET ASN ALA TYR PRO LEU VAL VAL THR PRO LEU VAL SER SEQRES 11 A 168 ALA GLY ILE PHE GLY VAL LYS PRO ALA VAL SER PHE ASP SEQRES 12 A 168 TYR LEU ILE ARG GLU ALA LYS THR ARG VAL LEU VAL VAL SEQRES 13 A 168 VAL ASN SER GLN ASP VAL TYR LYS SER LEU THR ILE HET ATP A 201 31 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 HOH *23(H2 O) HELIX 1 AA1 MET A 0 PHE A 5 5 6 HELIX 2 AA2 ASP A 20 TYR A 28 1 9 HELIX 3 AA3 GLY A 45 SER A 55 1 11 HELIX 4 AA4 GLY A 57 GLY A 71 1 15 HELIX 5 AA5 SER A 105 ALA A 113 1 9 HELIX 6 AA6 MET A 114 TYR A 117 5 4 HELIX 7 AA7 LYS A 133 ALA A 145 1 13 HELIX 8 AA8 SER A 155 THR A 163 1 9 SHEET 1 AA1 7 GLU A 6 VAL A 9 0 SHEET 2 AA1 7 VAL A 14 LEU A 18 -1 O LEU A 18 N GLU A 6 SHEET 3 AA1 7 ARG A 148 VAL A 153 1 O VAL A 151 N VAL A 17 SHEET 4 AA1 7 LEU A 119 THR A 122 1 N THR A 122 O VAL A 152 SHEET 5 AA1 7 VAL A 32 ALA A 37 1 N VAL A 34 O VAL A 121 SHEET 6 AA1 7 ASN A 89 VAL A 94 1 O ASN A 89 N LEU A 33 SHEET 7 AA1 7 SER A 78 GLN A 82 -1 N LEU A 81 O ILE A 90 SITE 1 AC1 13 ASP A 20 ALA A 21 ALA A 36 GLY A 46 SITE 2 AC1 13 ILE A 47 PRO A 123 LEU A 124 ALA A 127 SITE 3 AC1 13 GLY A 128 ILE A 129 VAL A 152 ASN A 154 SITE 4 AC1 13 HOH A 301 CRYST1 41.036 39.113 45.065 90.00 101.61 90.00 P 1 21 1 2 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 0.024369 0.000000 0.005008 0.00000 SCALE2 0.000000 0.025567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022654 0.00000