PDB Short entry for 5HB7 HEADER TRANSPORT PROTEIN 31-DEC-15 5HB7 TITLE CRYSTAL STRUCTURE OF CHAETOMIUM THERMOPHILUM NUP53 RRM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPORIN NUP53; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEAR PORE PROTEIN NUP53; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS SOURCE 3 144.50 / IMI 039719); SOURCE 4 ORGANISM_TAXID: 759272; SOURCE 5 STRAIN: DSM 1495 / CBS 144.50 / IMI 039719; SOURCE 6 GENE: NUP53, CTHT_0012410; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOCYTOPLASMIC TRANSPORT, PROTEIN TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.H.LIN,T.STUWE,A.HOELZ REVDAT 7 06-MAR-24 5HB7 1 REMARK REVDAT 6 25-DEC-19 5HB7 1 REMARK REVDAT 5 27-SEP-17 5HB7 1 REMARK REVDAT 4 20-SEP-17 5HB7 1 JRNL REMARK REVDAT 3 04-MAY-16 5HB7 1 JRNL REVDAT 2 27-APR-16 5HB7 1 JRNL REVDAT 1 20-APR-16 5HB7 0 JRNL AUTH D.H.LIN,T.STUWE,S.SCHILBACH,E.J.RUNDLET,T.PERRICHES,G.MOBBS, JRNL AUTH 2 Y.FAN,K.THIERBACH,F.M.HUBER,L.N.COLLINS,A.M.DAVENPORT, JRNL AUTH 3 Y.E.JEON,A.HOELZ JRNL TITL ARCHITECTURE OF THE SYMMETRIC CORE OF THE NUCLEAR PORE. JRNL REF SCIENCE V. 352 F1015 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27081075 JRNL DOI 10.1126/SCIENCE.AAF1015 REMARK 2 REMARK 2 RESOLUTION. 0.82 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 92709 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.118 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4651 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 38.6289 - 2.5450 0.98 3498 172 0.1371 0.1565 REMARK 3 2 2.5450 - 2.0201 0.99 3377 211 0.1253 0.1358 REMARK 3 3 2.0201 - 1.7647 0.97 3290 164 0.1270 0.1457 REMARK 3 4 1.7647 - 1.6034 0.99 3351 166 0.1213 0.1373 REMARK 3 5 1.6034 - 1.4885 0.98 3288 180 0.1142 0.1215 REMARK 3 6 1.4885 - 1.4007 0.99 3283 163 0.1103 0.1208 REMARK 3 7 1.4007 - 1.3305 0.95 3161 168 0.1076 0.1178 REMARK 3 8 1.3305 - 1.2726 0.98 3291 155 0.1035 0.1065 REMARK 3 9 1.2726 - 1.2236 0.98 3216 174 0.0969 0.1044 REMARK 3 10 1.2236 - 1.1814 0.98 3235 179 0.0873 0.0891 REMARK 3 11 1.1814 - 1.1445 0.97 3247 161 0.0833 0.1005 REMARK 3 12 1.1445 - 1.1117 0.95 3138 168 0.0815 0.0921 REMARK 3 13 1.1117 - 1.0825 0.97 3220 172 0.0844 0.0995 REMARK 3 14 1.0825 - 1.0561 0.96 3142 161 0.0859 0.0938 REMARK 3 15 1.0561 - 1.0321 0.96 3159 173 0.0873 0.0933 REMARK 3 16 1.0321 - 1.0101 0.94 3113 158 0.0917 0.1119 REMARK 3 17 1.0101 - 0.9899 0.94 3066 192 0.0933 0.1129 REMARK 3 18 0.9899 - 0.9712 0.94 3094 152 0.0996 0.1283 REMARK 3 19 0.9712 - 0.9539 0.91 2983 165 0.1053 0.1233 REMARK 3 20 0.9539 - 0.9377 0.93 3053 157 0.1080 0.1329 REMARK 3 21 0.9377 - 0.9226 0.91 2959 163 0.1166 0.1280 REMARK 3 22 0.9226 - 0.9084 0.89 2966 165 0.1215 0.1406 REMARK 3 23 0.9084 - 0.8950 0.90 2927 173 0.1273 0.1439 REMARK 3 24 0.8950 - 0.8824 0.88 2880 154 0.1378 0.1708 REMARK 3 25 0.8824 - 0.8705 0.82 2669 144 0.1488 0.1406 REMARK 3 26 0.8705 - 0.8592 0.71 2358 106 0.1630 0.1675 REMARK 3 27 0.8592 - 0.8484 0.63 2084 106 0.1795 0.1894 REMARK 3 28 0.8484 - 0.8382 0.59 1930 98 0.2019 0.2425 REMARK 3 29 0.8382 - 0.8285 0.53 1742 89 0.2223 0.2240 REMARK 3 30 0.8285 - 0.8191 0.40 1338 62 0.2656 0.2911 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) : 0.050 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.080 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 : 0.008 1241 REMARK 3 ANGLE : 1.062 1713 REMARK 3 CHIRALITY : 0.082 166 REMARK 3 PLANARITY : 0.009 244 REMARK 3 DIHEDRAL : 14.642 492 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 5HB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7293 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92712 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 33.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.0), 24 % (W/V) PEG REMARK 280 3350, 0.2 M POTASSIUM IODIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 17.49500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.01500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.18500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.01500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.49500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.18500 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 TOTAL BURIED SURFACE AREA: 410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 164 33.08 -96.52 REMARK 500 PRO A 170 39.69 -82.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 632 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A 633 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 634 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 635 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A 636 DISTANCE = 7.20 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HAX RELATED DB: PDB REMARK 900 RELATED ID: 5HAY RELATED DB: PDB REMARK 900 RELATED ID: 5HAZ RELATED DB: PDB REMARK 900 RELATED ID: 5HB1 RELATED DB: PDB REMARK 900 RELATED ID: 5HB2 RELATED DB: PDB REMARK 900 RELATED ID: 5HB0 RELATED DB: PDB REMARK 900 RELATED ID: 5HB3 RELATED DB: PDB REMARK 900 RELATED ID: 5HB4 RELATED DB: PDB REMARK 900 RELATED ID: 5HB5 RELATED DB: PDB REMARK 900 RELATED ID: 5HB6 RELATED DB: PDB REMARK 900 RELATED ID: 5HB8 RELATED DB: PDB DBREF 5HB7 A 133 253 UNP G0S156 NUP53_CHATD 133 253 SEQADV 5HB7 GLY A -4 UNP G0S156 EXPRESSION TAG SEQADV 5HB7 PRO A -3 UNP G0S156 EXPRESSION TAG SEQADV 5HB7 HIS A -2 UNP G0S156 EXPRESSION TAG SEQADV 5HB7 MET A -1 UNP G0S156 EXPRESSION TAG SEQRES 1 A 125 GLY PRO HIS MET PRO THR GLU VAL ILE LEU ARG GLY TYR SEQRES 2 A 125 ARG ASN ALA GLN HIS GLN TYR ALA ALA ILE ASN HIS TYR SEQRES 3 A 125 GLU GLN ILE ALA GLY ARG ILE CYS GLU ASP TYR PRO ARG SEQRES 4 A 125 GLU PRO PRO VAL GLU SER ARG ARG TYR LYS SER GLU LEU SEQRES 5 A 125 ARG ASP PRO ALA PHE THR HIS ARG ARG ALA LEU THR PRO SEQRES 6 A 125 GLU GLU ARG ALA LYS VAL ASN ARG ALA MET SER GLY GLU SEQRES 7 A 125 HIS TRP VAL LYS VAL THR PHE GLU SER ALA GLU ALA ALA SEQRES 8 A 125 ASP LYS ALA VAL TYR SER SER PRO GLN LEU ILE GLN GLY SEQRES 9 A 125 HIS LEU VAL TYR ALA GLU TYR TYR LYS GLY VAL PRO PRO SEQRES 10 A 125 ALA GLN ASP GLU ALA ILE PRO ASP HET IOD A 301 1 HET IOD A 302 1 HET IOD A 303 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 3(I 1-) FORMUL 5 HOH *236(H2 O) HELIX 1 AA1 ASN A 143 GLN A 145 5 3 HELIX 2 AA2 HIS A 146 GLY A 159 1 14 HELIX 3 AA3 THR A 192 ASN A 200 1 9 HELIX 4 AA4 SER A 215 SER A 226 1 12 SHEET 1 AA1 4 TRP A 208 PHE A 213 0 SHEET 2 AA1 4 THR A 134 ARG A 139 -1 N VAL A 136 O VAL A 211 SHEET 3 AA1 4 HIS A 233 TYR A 239 -1 O GLU A 238 N ILE A 137 SHEET 4 AA1 4 GLN A 228 ILE A 230 -1 N ILE A 230 O HIS A 233 CISPEP 1 SER A 226 PRO A 227 0 -6.19 SITE 1 AC1 2 GLN A 247 HOH A 533 SITE 1 AC2 3 ARG A 175 GLY A 232 HOH A 550 CRYST1 34.990 50.370 60.030 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 0.028580 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016658 0.00000