HEADER UNKNOWN FUNCTION 07-JUL-21 7P3A TITLE N-TERMINAL DOMAIN OF CGI-99 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA TRANSCRIPTION, TRANSLATION AND TRANSPORT FACTOR COMPND 3 PROTEIN; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: CLE7 HOMOLOG,CLE,HCLE; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SNA IS THE AFFINITY TAG CLEAVAGE SCAR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RTRAF, C14ORF166, CGI-99; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET HIS6 TEV LIC CLONING VECTOR (1B) KEYWDS CALPONIN HOMOLOGY DOMAIN, HCLE, RTRAF, C14ORF166, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.KROUPOVA,M.JINEK REVDAT 2 16-OCT-24 7P3A 1 REMARK REVDAT 1 22-DEC-21 7P3A 0 JRNL AUTH A.KROUPOVA,F.ACKLE,I.ASANOVIC,S.WEITZER,F.M.BONEBERG, JRNL AUTH 2 M.FAINI,A.LEITNER,A.CHUI,R.AEBERSOLD,J.MARTINEZ,M.JINEK JRNL TITL MOLECULAR ARCHITECTURE OF THE HUMAN TRNA LIGASE COMPLEX. JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34854379 JRNL DOI 10.7554/ELIFE.71656 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17235 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 864 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 4.5800 - 3.6400 1.00 2643 135 0.1455 0.1920 REMARK 3 2 3.6400 - 3.1800 1.00 2673 140 0.1713 0.2048 REMARK 3 3 3.1800 - 2.8900 1.00 2629 140 0.2009 0.2121 REMARK 3 4 2.8900 - 2.6800 1.00 2693 143 0.2070 0.2174 REMARK 3 5 2.6800 - 2.5200 1.00 2617 136 0.2159 0.2987 REMARK 3 6 2.5200 - 2.4000 1.00 2676 137 0.2135 0.2504 REMARK 3 7 2.4000 - 2.2900 1.00 2634 142 0.2285 0.2753 REMARK 3 8 2.2900 - 2.2000 1.00 2600 136 0.2411 0.2593 REMARK 3 9 2.2000 - 2.1300 1.00 2720 154 0.2515 0.2685 REMARK 3 10 2.1300 - 2.0600 1.00 2635 129 0.2669 0.3284 REMARK 3 11 2.0600 - 2.0000 1.00 2662 138 0.2999 0.3247 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) : 0.251 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.511 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.91 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 : 0.012 1765 REMARK 3 ANGLE : 1.106 2374 REMARK 3 CHIRALITY : 0.071 231 REMARK 3 PLANARITY : 0.006 308 REMARK 3 DIHEDRAL : 22.530 652 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 0 THROUGH 76 OR REMARK 3 (RESID 77 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 78 REMARK 3 THROUGH 94 OR RESID 201 THROUGH 221)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 0 THROUGH 94 OR REMARK 3 RESID 201 THROUGH 221)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7P3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292115085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0084 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.20 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 19.30 REMARK 200 R MERGE FOR SHELL (I) : 1.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.16_3549 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 200 MM MAGNESIUM REMARK 280 CHLORIDE, 20% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.64733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.29467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.47100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.11833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.82367 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A -1 REMARK 465 ASN A 95 REMARK 465 ALA A 96 REMARK 465 GLU A 97 REMARK 465 LYS A 98 REMARK 465 TYR A 99 REMARK 465 LYS A 100 REMARK 465 ASP A 101 REMARK 465 SER B -1 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 GLN B 77 CG CD OE1 NE2 REMARK 470 LYS B 98 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 ASN B 13 65.58 -116.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 7P3A A 2 101 UNP Q9Y224 RTRAF_HUMAN 2 101 DBREF 7P3A B 2 101 UNP Q9Y224 RTRAF_HUMAN 2 101 SEQADV 7P3A SER A -1 UNP Q9Y224 EXPRESSION TAG SEQADV 7P3A ASN A 0 UNP Q9Y224 EXPRESSION TAG SEQADV 7P3A ALA A 1 UNP Q9Y224 EXPRESSION TAG SEQADV 7P3A SER B -1 UNP Q9Y224 EXPRESSION TAG SEQADV 7P3A ASN B 0 UNP Q9Y224 EXPRESSION TAG SEQADV 7P3A ALA B 1 UNP Q9Y224 EXPRESSION TAG SEQRES 1 A 103 SER ASN ALA PHE ARG ARG LYS LEU THR ALA LEU ASP TYR SEQRES 2 A 103 HIS ASN PRO ALA GLY PHE ASN CYS LYS ASP GLU THR GLU SEQRES 3 A 103 PHE ARG ASN PHE ILE VAL TRP LEU GLU ASP GLN LYS ILE SEQRES 4 A 103 ARG HIS TYR LYS ILE GLU ASP ARG GLY ASN LEU ARG ASN SEQRES 5 A 103 ILE HIS SER SER ASP TRP PRO LYS PHE PHE GLU LYS TYR SEQRES 6 A 103 LEU ARG ASP VAL ASN CYS PRO PHE LYS ILE GLN ASP ARG SEQRES 7 A 103 GLN GLU ALA ILE ASP TRP LEU LEU GLY LEU ALA VAL ARG SEQRES 8 A 103 LEU GLU TYR GLY ASP ASN ALA GLU LYS TYR LYS ASP SEQRES 1 B 103 SER ASN ALA PHE ARG ARG LYS LEU THR ALA LEU ASP TYR SEQRES 2 B 103 HIS ASN PRO ALA GLY PHE ASN CYS LYS ASP GLU THR GLU SEQRES 3 B 103 PHE ARG ASN PHE ILE VAL TRP LEU GLU ASP GLN LYS ILE SEQRES 4 B 103 ARG HIS TYR LYS ILE GLU ASP ARG GLY ASN LEU ARG ASN SEQRES 5 B 103 ILE HIS SER SER ASP TRP PRO LYS PHE PHE GLU LYS TYR SEQRES 6 B 103 LEU ARG ASP VAL ASN CYS PRO PHE LYS ILE GLN ASP ARG SEQRES 7 B 103 GLN GLU ALA ILE ASP TRP LEU LEU GLY LEU ALA VAL ARG SEQRES 8 B 103 LEU GLU TYR GLY ASP ASN ALA GLU LYS TYR LYS ASP HET IPA A 201 12 HET IPA A 202 12 HET IPA A 203 12 HET MPD A 204 22 HET CL A 205 1 HET IPA B 201 12 HET IPA B 202 12 HET IPA B 203 12 HET MPD B 204 22 HET CL B 205 1 HETNAM IPA ISOPROPYL ALCOHOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM CL CHLORIDE ION HETSYN IPA 2-PROPANOL FORMUL 3 IPA 6(C3 H8 O) FORMUL 6 MPD 2(C6 H14 O2) FORMUL 7 CL 2(CL 1-) FORMUL 13 HOH *128(H2 O) HELIX 1 AA1 ASN A 0 HIS A 12 1 13 HELIX 2 AA2 PRO A 14 LYS A 36 1 23 HELIX 3 AA3 LYS A 41 ASP A 44 5 4 HELIX 4 AA4 ARG A 45 ASN A 50 1 6 HELIX 5 AA5 ASP A 55 VAL A 67 1 13 HELIX 6 AA6 ASP A 75 TYR A 92 1 18 HELIX 7 AA7 ALA B 1 ASN B 13 1 13 HELIX 8 AA8 ASN B 18 LYS B 36 1 19 HELIX 9 AA9 LYS B 41 ASP B 44 5 4 HELIX 10 AB1 ARG B 45 ASN B 50 1 6 HELIX 11 AB2 ASP B 55 VAL B 67 1 13 HELIX 12 AB3 ASP B 75 GLU B 97 1 23 HELIX 13 AB4 LYS B 98 ASP B 101 5 4 SSBOND 1 CYS A 19 CYS B 19 1555 1554 2.12 CRYST1 91.714 91.714 52.942 90.00 90.00 120.00 P 61 12 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 0.010903 0.006295 0.000000 0.00000 SCALE2 0.000000 0.012590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018889 0.00000