HEADER TRANSFERASE 04-APR-17 5NL8 TITLE PEX4 OF HANSENULA POLYMORPHA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-21 KDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME PEX4,PEROXIN-4,UBIQUITIN COMPND 5 CARRIER PROTEIN,UBIQUITIN-PROTEIN LIGASE; COMPND 6 EC: 2.3.2.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PICHIA ANGUSTA; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 870730; SOURCE 5 GENE: PEX4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM30 KEYWDS E3 LIGASE, LIGASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GROVES,C.WILLIAMS REVDAT 3 17-JAN-24 5NL8 1 REMARK REVDAT 2 14-FEB-18 5NL8 1 JRNL REVDAT 1 24-JAN-18 5NL8 0 JRNL AUTH M.R.GROVES,C.F.E.SCHROER,A.J.MIDDLETON,S.LUNEV,N.DANDA, JRNL AUTH 2 A.M.ALI,S.J.MARRINK,C.WILLIAMS JRNL TITL STRUCTURAL INSIGHTS INTO K48-LINKED UBIQUITIN CHAIN JRNL TITL 2 FORMATION BY THE PEX4P-PEX22P COMPLEX. JRNL REF BIOCHEM. BIOPHYS. RES. V. 496 562 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29288668 JRNL DOI 10.1016/J.BBRC.2017.12.150 REMARK 2 REMARK 2 RESOLUTION. 2.20 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 11654 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 584 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 45.2334 - 3.4917 1.00 3087 163 0.1826 0.2205 REMARK 3 2 3.4917 - 2.7716 0.99 2875 152 0.2327 0.3136 REMARK 3 3 2.7716 - 2.4213 0.90 2549 134 0.2366 0.2939 REMARK 3 4 2.4213 - 2.1999 0.91 2559 135 0.2902 0.3635 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.780 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 : 0.004 1517 REMARK 3 ANGLE : 0.796 2062 REMARK 3 CHIRALITY : 0.032 230 REMARK 3 PLANARITY : 0.004 261 REMARK 3 DIHEDRAL : 14.577 577 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 7.8065 -8.1476 -12.4062 REMARK 3 T TENSOR REMARK 3 T11: 0.1879 T22: 0.3442 REMARK 3 T33: 0.2305 T12: 0.0232 REMARK 3 T13: -0.0069 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 2.5815 L22: 1.2961 REMARK 3 L33: 2.2826 L12: -0.2306 REMARK 3 L13: -0.5553 L23: 0.8006 REMARK 3 S TENSOR REMARK 3 S11: -0.0840 S12: -0.3969 S13: 0.0327 REMARK 3 S21: 0.0953 S22: 0.0946 S23: 0.0562 REMARK 3 S31: -0.0026 S32: -0.0232 S33: 0.0002 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 5NL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03321 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14409 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 45.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 4.130 REMARK 200 R MERGE (I) : 0.14690 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.63 REMARK 200 R MERGE FOR SHELL (I) : 1.01400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2Y9M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.5 50% (V/V) PEG-200, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 103.20500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.17500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.60250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.17500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.17500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 154.80750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.17500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.17500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.60250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.17500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.17500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 154.80750 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 103.20500 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A 1 REMARK 465 ALA A 2 REMARK 465 MET A 3 REMARK 465 SER A 187 REMARK 465 ASN A 188 REMARK 465 ASP A 189 REMARK 465 VAL A 190 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 GLU A 23 141.92 -178.61 REMARK 500 GLU A 40 -100.20 -127.24 REMARK 500 PRO A 74 32.57 -97.27 REMARK 500 PRO A 151 1.50 -66.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NKZ RELATED DB: PDB DBREF 5NL8 A 5 190 UNP O60015 UBCX_PICAN 3 188 SEQADV 5NL8 GLY A 1 UNP O60015 EXPRESSION TAG SEQADV 5NL8 ALA A 2 UNP O60015 EXPRESSION TAG SEQADV 5NL8 MET A 3 UNP O60015 EXPRESSION TAG SEQADV 5NL8 ALA A 4 UNP O60015 EXPRESSION TAG SEQRES 1 A 190 GLY ALA MET ALA SER THR GLU LYS ARG LEU LEU LYS GLU SEQRES 2 A 190 TYR ARG ALA VAL LYS LYS GLU LEU THR GLU LYS ARG SER SEQRES 3 A 190 PRO ILE HIS ASP THR GLY ILE VAL ASP LEU HIS PRO LEU SEQRES 4 A 190 GLU ASP GLY LEU PHE ARG TRP SER ALA VAL ILE ARG GLY SEQRES 5 A 190 PRO ASP GLN SER PRO PHE GLU ASP ALA LEU TRP LYS LEU SEQRES 6 A 190 GLU ILE ASP ILE PRO THR ASN TYR PRO LEU ASP PRO PRO SEQRES 7 A 190 LYS ILE LYS PHE VAL VAL PHE GLY GLU GLU LYS ILE ARG SEQRES 8 A 190 GLN LEU GLN ARG LYS THR SER SER GLY ALA ARG LYS VAL SEQRES 9 A 190 CYS TYR LYS MET PRO HIS PRO ASN VAL ASN PHE LYS THR SEQRES 10 A 190 GLY GLU ILE CYS LEU ASP ILE LEU GLN GLN LYS TRP SER SEQRES 11 A 190 PRO ALA TRP THR LEU GLN SER ALA LEU VAL ALA ILE VAL SEQRES 12 A 190 VAL LEU LEU ALA ASN PRO GLU PRO LEU SER PRO LEU ASN SEQRES 13 A 190 ILE ASP MET ALA ASN LEU LEU LYS CYS ASP ASP THR THR SEQRES 14 A 190 ALA TYR LYS ASP LEU VAL HIS TYR TYR ILE ALA LYS TYR SEQRES 15 A 190 SER ALA TYR GLU SER ASN ASP VAL FORMUL 2 HOH *55(H2 O) HELIX 1 AA1 SER A 5 THR A 22 1 18 HELIX 2 AA2 SER A 26 THR A 31 5 6 HELIX 3 AA3 GLY A 86 ARG A 95 1 10 HELIX 4 AA4 LEU A 122 GLN A 127 1 6 HELIX 5 AA5 THR A 134 ASN A 148 1 15 HELIX 6 AA6 ASN A 156 CYS A 165 1 10 HELIX 7 AA7 ASP A 167 TYR A 182 1 16 SHEET 1 AA1 4 ILE A 33 PRO A 38 0 SHEET 2 AA1 4 ARG A 45 ARG A 51 -1 O SER A 47 N HIS A 37 SHEET 3 AA1 4 LEU A 62 ASP A 68 -1 O TRP A 63 N ILE A 50 SHEET 4 AA1 4 LYS A 79 PHE A 82 -1 O LYS A 79 N ASP A 68 SHEET 1 AA2 2 VAL A 104 CYS A 105 0 SHEET 2 AA2 2 SER A 183 ALA A 184 -1 O ALA A 184 N VAL A 104 CISPEP 1 TYR A 73 PRO A 74 0 3.02 CRYST1 46.350 46.350 206.410 90.00 90.00 90.00 P 41 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 0.021575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004845 0.00000