HEADER HYDROLASE 24-OCT-18 6MV7 TITLE CRYSTAL STRUCTURE OF RNASE 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE K6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE K6; COMPND 5 EC: 3.1.27.-; COMPND 6 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: RNASE6, RNS6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASE, NUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-F.COUTURE,N.DOUCET REVDAT 4 11-OCT-23 6MV7 1 REMARK REVDAT 3 27-MAY-20 6MV7 1 JRNL REVDAT 2 15-JAN-20 6MV7 1 REMARK ATOM REVDAT 1 13-NOV-19 6MV7 0 JRNL AUTH C.NARAYANAN,D.N.BERNARD,M.LETOURNEAU,J.GAGNON,D.GAGNE, JRNL AUTH 2 K.BAFNA,C.CALMETTES,J.F.COUTURE,P.K.AGARWAL,N.DOUCET JRNL TITL INSIGHTS INTO STRUCTURAL AND DYNAMICAL CHANGES EXPERIENCED JRNL TITL 2 BY HUMAN RNASE 6 UPON LIGAND BINDING. JRNL REF BIOCHEMISTRY V. 59 755 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 31909602 JRNL DOI 10.1021/ACS.BIOCHEM.9B00888 REMARK 2 REMARK 2 RESOLUTION. 2.59 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 3537 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 354 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 36.0950 - 3.7343 1.00 1132 126 0.1998 0.2198 REMARK 3 2 3.7343 - 2.9645 0.99 1038 115 0.2190 0.2673 REMARK 3 3 2.9645 - 2.5900 0.97 1013 113 0.2460 0.2931 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.04 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 : 0.003 1083 REMARK 3 ANGLE : 0.703 1481 REMARK 3 CHIRALITY : 0.041 157 REMARK 3 PLANARITY : 0.004 189 REMARK 3 DIHEDRAL : 13.497 660 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 6MV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-16 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 : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 36.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71 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) : 0.10400 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: PHASER REMARK 200 STARTING MODEL: 6MV6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, 50MM SODIUM PHOSPHATE, VAPOR REMARK 280 DIFFUSION, 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 13.82500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.96000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.96000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.82500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.41500 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 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 LYS A 3 CG CD CE NZ REMARK 470 GLN A 17 CG CD OE1 NE2 REMARK 470 SER A 19 OG REMARK 470 ARG A 25 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 LYS A 87 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 4 CZ 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 117 O HOH A 301 2.08 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 CD2 HIS A 67 NZ LYS A 111 3445 2.06 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 AMP A 201 DBREF 6MV7 A 1 127 UNP Q93091 RNAS6_HUMAN 24 150 SEQADV 6MV7 MET A 0 UNP Q93091 INITIATING METHIONINE SEQRES 1 A 128 MET TRP PRO LYS ARG LEU THR LYS ALA HIS TRP PHE GLU SEQRES 2 A 128 ILE GLN HIS ILE GLN PRO SER PRO LEU GLN CYS ASN ARG SEQRES 3 A 128 ALA MET SER GLY ILE ASN ASN TYR THR GLN HIS CYS LYS SEQRES 4 A 128 HIS GLN ASN THR PHE LEU HIS ASP SER PHE GLN ASN VAL SEQRES 5 A 128 ALA ALA VAL CYS ASP LEU LEU SER ILE VAL CYS LYS ASN SEQRES 6 A 128 ARG ARG HIS ASN CYS HIS GLN SER SER LYS PRO VAL ASN SEQRES 7 A 128 MET THR ASP CYS ARG LEU THR SER GLY LYS TYR PRO GLN SEQRES 8 A 128 CYS ARG TYR SER ALA ALA ALA GLN TYR LYS PHE PHE ILE SEQRES 9 A 128 VAL ALA CYS ASP PRO PRO GLN LYS SER ASP PRO PRO TYR SEQRES 10 A 128 LYS LEU VAL PRO VAL HIS LEU ASP SER ILE LEU HET AMP A 201 23 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 HOH *27(H2 O) HELIX 1 AA1 THR A 6 ILE A 16 1 11 HELIX 2 AA2 GLN A 22 GLN A 35 1 14 HELIX 3 AA3 SER A 47 CYS A 55 1 9 SHEET 1 AA1 5 GLN A 40 LEU A 44 0 SHEET 2 AA1 5 VAL A 76 SER A 85 -1 O CYS A 81 N ASN A 41 SHEET 3 AA1 5 ARG A 92 ASP A 107 -1 O GLN A 98 N MET A 78 SHEET 4 AA1 5 CYS A 69 GLN A 71 -1 N HIS A 70 O VAL A 104 SHEET 5 AA1 5 SER A 59 ILE A 60 -1 N ILE A 60 O CYS A 69 SHEET 1 AA2 4 GLN A 40 LEU A 44 0 SHEET 2 AA2 4 VAL A 76 SER A 85 -1 O CYS A 81 N ASN A 41 SHEET 3 AA2 4 ARG A 92 ASP A 107 -1 O GLN A 98 N MET A 78 SHEET 4 AA2 4 VAL A 119 LEU A 127 -1 O VAL A 121 N ALA A 105 SSBOND 1 CYS A 23 CYS A 81 1555 1555 2.03 SSBOND 2 CYS A 37 CYS A 91 1555 1555 2.03 SSBOND 3 CYS A 55 CYS A 106 1555 1555 2.03 SSBOND 4 CYS A 62 CYS A 69 1555 1555 2.03 CISPEP 1 TYR A 88 PRO A 89 0 4.17 SITE 1 AC1 12 LYS A 7 VAL A 61 CYS A 62 ASN A 64 SITE 2 AC1 12 ARG A 66 HIS A 67 ASN A 68 ALA A 105 SITE 3 AC1 12 ASP A 107 VAL A 121 HIS A 122 HOH A 319 CRYST1 27.650 38.830 97.920 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 0.036166 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010212 0.00000