HEADER HYDROLASE 28-NOV-13 4NSP TITLE CRYSTAL STRUCTURE OF HUMAN ENDOV COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE V; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: HENDOV, INOSINE-SPECIFIC ENDORIBONUCLEASE; COMPND 6 EC: 3.1.26.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ENDOV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS RAASE H-LIKE MOTIF, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,Z.ZHANG,Z.HAO REVDAT 3 20-SEP-23 4NSP 1 SEQADV REVDAT 2 24-SEP-14 4NSP 1 JRNL REVDAT 1 10-SEP-14 4NSP 0 JRNL AUTH Z.ZHANG,Z.HAO,Z.WANG,Q.LI,W.XIE JRNL TITL STRUCTURE OF HUMAN ENDONUCLEASE V AS AN INOSINE-SPECIFIC JRNL TITL 2 RIBONUCLEASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 2286 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25195743 JRNL DOI 10.1107/S139900471401356X REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 9803 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 471 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 26.7570 - 3.3159 0.98 3162 165 0.1874 0.2300 REMARK 3 2 3.3159 - 2.6326 1.00 3107 152 0.2301 0.3078 REMARK 3 3 2.6326 - 2.3001 1.00 3063 154 0.2346 0.3096 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 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 : 0.004 1881 REMARK 3 ANGLE : 0.889 2544 REMARK 3 CHIRALITY : 0.063 294 REMARK 3 PLANARITY : 0.003 329 REMARK 3 DIHEDRAL : 14.171 703 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 4NSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083607. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 7.5 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 : NOVA HIGH-FLUX-MICRO-FOCUS REMARK 200 SEALED TUBE 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 : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9828 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 26.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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: PDB ENTRY 3HD0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM FORMATE, 0.1 M TRIS-HCL REMARK 280 PH7.5,19%PEG3350, EVAPORATION, TEMPERATURE 298K 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 19.87500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.26550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.35650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.26550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.87500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.35650 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: 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 MET A 12 REMARK 465 LYS A 57 REMARK 465 GLY A 58 REMARK 465 ALA A 253 REMARK 465 LEU A 254 REMARK 465 GLU A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 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 ARG A 248 CG CD NE CZ NH1 NH2 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 NE2 GLN A 110 O HOH A 382 2.03 REMARK 500 O ARG A 23 O HOH A 369 2.13 REMARK 500 OH TYR A 79 O HOH A 382 2.19 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 VAL A 61 -63.85 -125.31 REMARK 500 LYS A 114 -61.74 -99.96 REMARK 500 GLU A 115 68.78 -118.52 REMARK 500 LEU A 131 83.70 -68.53 REMARK 500 PHE A 136 67.21 -161.17 REMARK 500 ARG A 179 109.38 -56.91 REMARK 500 PHE A 230 -164.66 -125.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 4NSP A 13 250 UNP Q8N8Q3 ENDOV_HUMAN 13 250 SEQADV 4NSP MET A 12 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP ALA A 251 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP ALA A 252 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP ALA A 253 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP LEU A 254 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP GLU A 255 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP HIS A 256 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP HIS A 257 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP HIS A 258 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP HIS A 259 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP HIS A 260 UNP Q8N8Q3 EXPRESSION TAG SEQADV 4NSP HIS A 261 UNP Q8N8Q3 EXPRESSION TAG SEQRES 1 A 250 MET THR LEU SER LEU TRP LYS ARG GLU GLN ALA ARG LEU SEQRES 2 A 250 LYS ALA HIS VAL VAL ASP ARG ASP THR GLU ALA TRP GLN SEQRES 3 A 250 ARG ASP PRO ALA PHE SER GLY LEU GLN ARG VAL GLY GLY SEQRES 4 A 250 VAL ASP VAL SER PHE VAL LYS GLY ASP SER VAL ARG ALA SEQRES 5 A 250 CYS ALA SER LEU VAL VAL LEU SER PHE PRO GLU LEU GLU SEQRES 6 A 250 VAL VAL TYR GLU GLU SER ARG MET VAL SER LEU THR ALA SEQRES 7 A 250 PRO TYR VAL SER GLY PHE LEU ALA PHE ARG GLU VAL PRO SEQRES 8 A 250 PHE LEU LEU GLU LEU VAL GLN GLN LEU ARG GLU LYS GLU SEQRES 9 A 250 PRO GLY LEU MET PRO GLN VAL LEU LEU VAL ASP GLY ASN SEQRES 10 A 250 GLY VAL LEU HIS HIS ARG GLY PHE GLY VAL ALA CYS HIS SEQRES 11 A 250 LEU GLY VAL LEU THR ASP LEU PRO CYS VAL GLY VAL ALA SEQRES 12 A 250 LYS LYS LEU LEU GLN VAL ASP GLY LEU GLU ASN ASN ALA SEQRES 13 A 250 LEU HIS LYS GLU LYS ILE ARG LEU LEU GLN THR ARG GLY SEQRES 14 A 250 ASP SER PHE PRO LEU LEU GLY ASP SER GLY THR VAL LEU SEQRES 15 A 250 GLY MET ALA LEU ARG SER HIS ASP ARG SER THR ARG PRO SEQRES 16 A 250 LEU TYR ILE SER VAL GLY HIS ARG MET SER LEU GLU ALA SEQRES 17 A 250 ALA VAL ARG LEU THR CYS CYS CYS CYS ARG PHE ARG ILE SEQRES 18 A 250 PRO GLU PRO VAL ARG GLN ALA ASP ILE CYS SER ARG GLU SEQRES 19 A 250 HIS ILE ARG LYS SER ALA ALA ALA LEU GLU HIS HIS HIS SEQRES 20 A 250 HIS HIS HIS FORMUL 2 HOH *84(H2 O) HELIX 1 1 LEU A 14 ALA A 26 1 13 HELIX 2 2 GLU A 34 ASP A 39 5 6 HELIX 3 3 LEU A 96 GLU A 115 1 20 HELIX 4 4 PRO A 116 MET A 119 5 4 HELIX 5 5 GLY A 137 ASP A 147 1 11 HELIX 6 6 ASN A 166 LEU A 176 1 11 HELIX 7 7 SER A 216 CYS A 227 1 12 HELIX 8 8 PRO A 233 ALA A 252 1 20 SHEET 1 A 8 VAL A 77 SER A 86 0 SHEET 2 A 8 ARG A 62 SER A 71 -1 N VAL A 69 O VAL A 78 SHEET 3 A 8 ARG A 47 PHE A 55 -1 N ASP A 52 O SER A 66 SHEET 4 A 8 VAL A 122 ASP A 126 1 O VAL A 122 N GLY A 49 SHEET 5 A 8 CYS A 150 ALA A 154 1 O VAL A 153 N VAL A 125 SHEET 6 A 8 LEU A 207 HIS A 213 -1 O HIS A 213 N CYS A 150 SHEET 7 A 8 VAL A 192 LEU A 197 -1 N LEU A 197 O LEU A 207 SHEET 8 A 8 SER A 182 LEU A 186 -1 N PHE A 183 O ALA A 196 CISPEP 1 PHE A 72 PRO A 73 0 2.74 CRYST1 39.750 48.713 108.531 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 0.025157 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020528 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009214 0.00000