HEADER TRANSLATION 05-AUG-19 6KNE TITLE THE C-TERMINAL DOMAIN OF TRANSLATION INITIATION FACTOR 5 AT HIGH PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATION INITIATION FACTOR EIF5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS; SOURCE 3 ORGANISM_TAXID: 5476; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INITIATION FACTOR, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR Y.JIAN,Y.YUXIN,Y.MIN REVDAT 2 27-MAR-24 6KNE 1 REMARK REVDAT 1 17-JUN-20 6KNE 0 JRNL AUTH Y.YE,M.CHEN,K.KATO,M.YAO JRNL TITL THE PH-DEPENDENT CONFORMATIONAL CHANGE OF EUKARYOTIC JRNL TITL 2 TRANSLATION INITIATION FACTOR 5: INSIGHTS INTO JRNL TITL 3 PARTNER-BINDING MANNER. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 519 186 2019 JRNL REFN ESSN 1090-2104 JRNL PMID 31492496 JRNL DOI 10.1016/J.BBRC.2019.08.128 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 19086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 983 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 41.1470 - 3.2531 0.98 2731 153 0.1985 0.2216 REMARK 3 2 3.2531 - 2.5822 0.98 2628 124 0.2494 0.2668 REMARK 3 3 2.5822 - 2.2558 0.99 2585 144 0.2466 0.3195 REMARK 3 4 2.2558 - 2.0496 0.99 2597 143 0.2656 0.3338 REMARK 3 5 2.0496 - 1.9027 0.98 2530 141 0.3019 0.4025 REMARK 3 6 1.9027 - 1.7905 0.97 2493 155 0.3143 0.3767 REMARK 3 7 1.7905 - 1.7010 0.98 2539 123 0.3650 0.4074 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.09 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 : 0.007 1394 REMARK 3 ANGLE : 0.985 1879 REMARK 3 CHIRALITY : 0.037 204 REMARK 3 PLANARITY : 0.005 245 REMARK 3 DIHEDRAL : 15.462 537 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 6KNE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 41.147 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.534 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.55 REMARK 200 R MERGE FOR SHELL (I) : 0.50800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.710 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE PH 5.5, 40% (V/V) PEG REMARK 280 600, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 24.97500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.64250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.07800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.64250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.97500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.07800 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 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 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 ASP A 310 -149.55 -133.70 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6KNE A 257 418 UNP A0A1D8PNF5_CANAL DBREF2 6KNE A A0A1D8PNF5 257 418 SEQADV 6KNE GLY A 250 UNP A0A1D8PNF EXPRESSION TAG SEQADV 6KNE HIS A 251 UNP A0A1D8PNF EXPRESSION TAG SEQADV 6KNE MET A 252 UNP A0A1D8PNF EXPRESSION TAG SEQADV 6KNE GLY A 253 UNP A0A1D8PNF EXPRESSION TAG SEQADV 6KNE LEU A 254 UNP A0A1D8PNF EXPRESSION TAG SEQADV 6KNE SER A 255 UNP A0A1D8PNF EXPRESSION TAG SEQADV 6KNE VAL A 256 UNP A0A1D8PNF EXPRESSION TAG SEQRES 1 A 169 GLY HIS MET GLY LEU SER VAL GLN ASN ASN LYS PHE ASP SEQRES 2 A 169 GLU PHE GLY GLU TRP LEU LEU LYS GLU SER ASN GLY SER SEQRES 3 A 169 LYS ASP ASP LEU PRO SER ASP VAL GLU ILE TYR LYS ARG SEQRES 4 A 169 ILE VAL GLU LEU GLU ILE ALA ASP THR PRO GLU THR LEU SEQRES 5 A 169 GLN VAL LEU GLY GLN VAL LEU PHE ASP ASP ASP ILE ILE SEQRES 6 A 169 ASN GLN ILE GLU PRO HIS VAL GLY LEU LEU THR LYS LEU SEQRES 7 A 169 ILE ASN GLY ASP GLU GLU PHE GLU LYS ALA LEU LEU GLY SEQRES 8 A 169 GLY LEU GLU ARG PHE PHE GLY LEU GLU LYS PRO ASN LEU SEQRES 9 A 169 ILE PRO GLN ILE PRO LYS ILE LEU HIS GLY PHE TYR ASP SEQRES 10 A 169 ARG ASP LEU ILE SER GLU GLU VAL LEU ILE LYS TRP GLY SEQRES 11 A 169 SER LYS VAL SER LYS LYS TYR VAL PRO LYS ASP VAL SER SEQRES 12 A 169 LYS LYS VAL ARG LYS ALA ALA LYS PRO PHE VAL LYS TRP SEQRES 13 A 169 LEU GLN GLU ALA GLU GLU GLU GLU GLU GLU GLU SER ASP FORMUL 2 HOH *64(H2 O) HELIX 1 AA1 ASN A 259 ASN A 273 1 15 HELIX 2 AA2 SER A 275 LEU A 279 5 5 HELIX 3 AA3 SER A 281 LEU A 292 1 12 HELIX 4 AA4 PRO A 298 LEU A 308 1 11 HELIX 5 AA5 ASP A 312 GLN A 316 5 5 HELIX 6 AA6 ILE A 317 PRO A 319 5 3 HELIX 7 AA7 HIS A 320 ASN A 329 1 10 HELIX 8 AA8 ASP A 331 GLU A 349 1 19 HELIX 9 AA9 LYS A 350 PRO A 355 5 6 HELIX 10 AB1 GLN A 356 ARG A 367 1 12 HELIX 11 AB2 SER A 371 GLY A 379 1 9 HELIX 12 AB3 PRO A 388 ALA A 399 1 12 HELIX 13 AB4 ALA A 399 GLU A 410 1 12 HELIX 14 AB5 GLU A 411 GLU A 414 5 4 CISPEP 1 GLY A 250 HIS A 251 0 6.44 CRYST1 49.950 54.156 63.285 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 0.020020 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015802 0.00000