HEADER RNA BINDING PROTEIN 05-OCT-19 6L2L TITLE THE STRUCTURE OF THE TRNA-SPECIFIC DEAMINASE FROM M. CAPRICOLUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DEAMINASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRNA-SPECIFIC DEAMINASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA CAPRICOLUM SUBSP. CAPRICOLUM; SOURCE 3 ORGANISM_TAXID: 40479; SOURCE 4 GENE: MCGM508_01875; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRNA-SPECIFIC DEAMINASE, PROTEIN ENGINEERING, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,H.LIU,S.WU REVDAT 2 22-NOV-23 6L2L 1 REMARK REVDAT 1 12-AUG-20 6L2L 0 JRNL AUTH H.LIU,S.WU,D.RAN,W.XIE JRNL TITL STRUCTURE OF A TRNA-SPECIFIC DEAMINASE WITH COMPROMISED JRNL TITL 2 DEAMINATION ACTIVITY. JRNL REF BIOCHEM.J. V. 477 1483 2020 JRNL REFN ESSN 1470-8728 JRNL PMID 32270856 JRNL DOI 10.1042/BCJ20190858 REMARK 2 REMARK 2 RESOLUTION. 2.40 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.355 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 7649 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.955 REMARK 3 FREE R VALUE TEST SET COUNT : 379 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 21.0650 - 3.4587 1.00 2527 142 0.1665 0.1790 REMARK 3 2 3.4587 - 2.7472 1.00 2366 132 0.2058 0.2477 REMARK 3 3 2.7472 - 2.4005 1.00 2377 105 0.2316 0.3305 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) : 0.283 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.772 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.47 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 : 0.005 1179 REMARK 3 ANGLE : 0.682 1583 REMARK 3 CHIRALITY : 0.047 186 REMARK 3 PLANARITY : 0.002 199 REMARK 3 DIHEDRAL : 13.070 730 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 6L2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300013659. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 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 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 : 7697 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 21.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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: 2A8N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.49M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE, 0.91M POTASSIUM PHOSPHATE DIBASIC, PH 6.9, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.96550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.56900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.56900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 110.94825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.56900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.56900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.98275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.56900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.56900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 110.94825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.56900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.56900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.98275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.96550 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: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1 REMARK 465 SER A 115 REMARK 465 ILE A 116 REMARK 465 ASN A 117 REMARK 465 ASP A 118 REMARK 465 GLU A 149 REMARK 465 HIS A 150 REMARK 465 HIS A 151 REMARK 465 HIS A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 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 ILE A 110 CG1 CG2 CD1 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 LYS A 127 CG CD CE NZ 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 PRO A 25 94.34 -65.37 REMARK 500 SER A 44 33.14 -145.40 REMARK 500 GLN A 53 43.55 -80.12 REMARK 500 ASN A 128 73.29 -165.94 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 54 ND1 REMARK 620 2 CYS A 84 SG 109.4 REMARK 620 3 CYS A 87 SG 116.8 116.1 REMARK 620 4 HOH A 337 O 97.4 109.5 105.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 DBREF1 6L2L A 1 147 UNP A0A0C2W6A5_MYCCA DBREF2 6L2L A A0A0C2W6A5 1 147 SEQADV 6L2L LEU A 148 UNP A0A0C2W6A EXPRESSION TAG SEQADV 6L2L GLU A 149 UNP A0A0C2W6A EXPRESSION TAG SEQADV 6L2L HIS A 150 UNP A0A0C2W6A EXPRESSION TAG SEQADV 6L2L HIS A 151 UNP A0A0C2W6A EXPRESSION TAG SEQADV 6L2L HIS A 152 UNP A0A0C2W6A EXPRESSION TAG SEQADV 6L2L HIS A 153 UNP A0A0C2W6A EXPRESSION TAG SEQADV 6L2L HIS A 154 UNP A0A0C2W6A EXPRESSION TAG SEQADV 6L2L HIS A 155 UNP A0A0C2W6A EXPRESSION TAG SEQRES 1 A 155 MET ASP ASP PHE ASN ASN ILE LEU ASP LEU LEU ILE ASN SEQRES 2 A 155 GLU SER LYS LYS ALA ILE LYS HIS ASN ASP ILE PRO VAL SEQRES 3 A 155 SER CYS CYS ILE ILE ASP SER ASN ASN ASN ILE LEU SER SEQRES 4 A 155 LEU ALA ILE ASN SER ARG TYR LYS ASN LYS ASP ILE SER SEQRES 5 A 155 GLN HIS ALA GLU ILE ASN VAL ILE ASN ASP LEU ILE SER SEQRES 6 A 155 LYS LEU ASN SER PHE ASN LEU SER LYS TYR LYS LEU ILE SEQRES 7 A 155 THR THR LEU GLU PRO CYS MET MET CYS TYR SER ALA ILE SEQRES 8 A 155 LYS GLN VAL LYS ILE ASN THR ILE TYR TYR LEU VAL ASP SEQRES 9 A 155 SER TYR LYS PHE GLY ILE LYS ASN ASN TYR SER ILE ASN SEQRES 10 A 155 ASP GLN ASN LEU ASN LEU ILE GLN ILE LYS ASN GLN LYS SEQRES 11 A 155 LYS GLN SER GLU TYR ILE LYS LEU LEU ASN ILE PHE PHE SEQRES 12 A 155 ILE ASN LYS ARG LEU GLU HIS HIS HIS HIS HIS HIS HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *59(H2 O) HELIX 1 AA1 PHE A 4 LYS A 16 1 13 HELIX 2 AA2 LYS A 17 ASN A 22 5 6 HELIX 3 AA3 SER A 44 LYS A 49 1 6 HELIX 4 AA4 HIS A 54 ASN A 68 1 15 HELIX 5 AA5 CYS A 84 VAL A 94 1 11 HELIX 6 AA6 ASN A 128 LEU A 148 1 21 SHEET 1 AA1 5 ILE A 37 ILE A 42 0 SHEET 2 AA1 5 SER A 27 ILE A 31 -1 N ILE A 30 O LEU A 38 SHEET 3 AA1 5 LYS A 76 LEU A 81 -1 O ILE A 78 N CYS A 29 SHEET 4 AA1 5 THR A 98 VAL A 103 1 O TYR A 100 N LEU A 77 SHEET 5 AA1 5 ASN A 122 GLN A 125 1 O ILE A 124 N TYR A 101 LINK ND1 HIS A 54 ZN ZN A 201 1555 1555 2.05 LINK SG CYS A 84 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 87 ZN ZN A 201 1555 1555 2.25 LINK ZN ZN A 201 O HOH A 337 1555 1555 2.16 SITE 1 AC1 4 HIS A 54 CYS A 84 CYS A 87 HOH A 337 CRYST1 49.138 49.138 147.931 90.00 90.00 90.00 P 43 21 2 8 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 0.020351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020351 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006760 0.00000