HEADER TRANSCRIPTION 17-MAY-18 5ZX1 TITLE CRYSTAL STRUCTURE OF ENT DOMAIN FROM T. BRUCEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ENT DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI; SOURCE 3 ORGANISM_TAXID: 185431; SOURCE 4 STRAIN: 927/4 GUTAT10.1; SOURCE 5 GENE: TB11.02.2890; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENT DOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR L.SHANHUI,T.XIAOMING,M.JUAN REVDAT 3 22-NOV-23 5ZX1 1 REMARK REVDAT 2 02-DEC-20 5ZX1 1 JRNL REVDAT 1 22-MAY-19 5ZX1 0 JRNL AUTH J.MI,X.YANG,J.ZHANG,X.ZHANG,C.XU,S.LIAO,X.TU JRNL TITL CRYSTAL STRUCTURE OF AN ENT DOMAIN FROM TRYPANOSOMA BRUCEI. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 505 755 2018 JRNL REFN ESSN 1090-2104 JRNL PMID 30293681 JRNL DOI 10.1016/J.BBRC.2018.09.167 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13-2998 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) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 8068 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 421 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 2.3900 - 2.3100 1.00 0 0 0.3499 0.3723 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 5ZX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007809. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8072 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310 REMARK 200 RESOLUTION RANGE LOW (A) : 46.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL 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: PHENIX 1.13-2998 REMARK 200 STARTING MODEL: 1UZ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M L-PROLINE, 0.1M HEPES PH7.5, 10% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 66.29500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 66.29500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.01500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 66.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.00750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 66.29500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.02250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 66.29500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.02250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.29500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 10.00750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 66.29500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 66.29500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 20.01500 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 66.29500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 66.29500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 20.01500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 66.29500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 30.02250 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 66.29500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 10.00750 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 66.29500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 10.00750 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 66.29500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 30.02250 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 66.29500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 66.29500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 20.01500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 219 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 241 LIES ON A SPECIAL POSITION. 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 -13 REMARK 465 SER A -12 REMARK 465 ALA A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 VAL A -6 REMARK 465 ALA A -5 REMARK 465 ALA A -4 REMARK 465 ILE A -3 REMARK 465 TYR A -2 REMARK 465 GLY A -1 REMARK 465 ARG A 0 REMARK 465 ALA A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 4 REMARK 465 GLN A 5 REMARK 465 ASN A 6 REMARK 465 ALA A 7 REMARK 465 PRO A 8 REMARK 465 VAL A 9 REMARK 465 LYS A 10 REMARK 465 LEU A 11 REMARK 465 GLN A 12 REMARK 465 PRO A 13 REMARK 465 HIS A 98 REMARK 465 HIS A 99 REMARK 465 HIS A 100 REMARK 465 HIS A 101 REMARK 465 HIS A 102 REMARK 465 HIS A 103 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 NH2 ARG A 92 O HOH A 201 2.14 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 O HOH A 236 O HOH A 252 8666 2.16 REMARK 500 O HOH A 217 O HOH A 247 8666 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 5ZX1 A -13 95 UNP Q385P5 Q385P5_TRYB2 1 109 SEQADV 5ZX1 LEU A 96 UNP Q385P5 EXPRESSION TAG SEQADV 5ZX1 GLU A 97 UNP Q385P5 EXPRESSION TAG SEQADV 5ZX1 HIS A 98 UNP Q385P5 EXPRESSION TAG SEQADV 5ZX1 HIS A 99 UNP Q385P5 EXPRESSION TAG SEQADV 5ZX1 HIS A 100 UNP Q385P5 EXPRESSION TAG SEQADV 5ZX1 HIS A 101 UNP Q385P5 EXPRESSION TAG SEQADV 5ZX1 HIS A 102 UNP Q385P5 EXPRESSION TAG SEQADV 5ZX1 HIS A 103 UNP Q385P5 EXPRESSION TAG SEQRES 1 A 117 MET SER ALA SER GLY SER GLY VAL ALA ALA ILE TYR GLY SEQRES 2 A 117 ARG ALA GLU GLU ALA GLN ASN ALA PRO VAL LYS LEU GLN SEQRES 3 A 117 PRO VAL PRO ALA PHE GLU LEU TYR LYS ALA ALA ARG GLU SEQRES 4 A 117 GLU GLU LEU CYS SER TYR ARG SER LEU CYS ARG VAL LEU SEQRES 5 A 117 CYS MET HIS SER GLY GLY LYS LEU THR LYS GLN GLN ARG SEQRES 6 A 117 ARG ILE LEU GLU ASP MET ARG GLU GLU LEU CYS LEU PRO SEQRES 7 A 117 THR GLU ARG ALA GLU ALA GLU LEU ALA ALA ALA ARG GLU SEQRES 8 A 117 ASP VAL LEU VAL THR SER VAL ALA ALA SER GLY VAL LEU SEQRES 9 A 117 LYS ARG ARG GLN ASP LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *52(H2 O) HELIX 1 AA1 PRO A 15 GLY A 43 1 29 HELIX 2 AA2 THR A 47 LEU A 61 1 15 HELIX 3 AA3 PRO A 64 ASP A 78 1 15 HELIX 4 AA4 ASP A 78 GLY A 88 1 11 HELIX 5 AA5 VAL A 89 LYS A 91 5 3 HELIX 6 AA6 ARG A 92 GLU A 97 1 6 CRYST1 132.590 132.590 40.030 90.00 90.00 90.00 I 41 2 2 16 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 0.007542 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007542 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024981 0.00000