HEADER PROTEIN TRANSPORT 22-NOV-13 4NPN TITLE CRYSTAL STRUCTURE OF HUMAN TETRA-SUMO-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DELTAN11SUMO-2, UNP RESIDUES 12-93; COMPND 5 SYNONYM: SUMO-2, HSMT3, SMT3 HOMOLOG 2, SUMO-3, SENTRIN-2, UBIQUITIN- COMPND 6 LIKE PROTEIN SMT3A, SMT3A; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SMT3A, SMT3H2, SUMO2, SUMO2 SMT3A SMT3H2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PROTEIN BINDING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.C.-H.KUNG,M.T.NAIK,C.L.CHEN,C.MA,T.H.HUANG REVDAT 2 20-MAR-24 4NPN 1 SEQADV REVDAT 1 15-OCT-14 4NPN 0 JRNL AUTH C.C.-H.KUNG,M.T.NAIK,S.H.WANG,H.M.SHIH,C.C.CHANG,L.Y.LIN, JRNL AUTH 2 C.L.CHEN,C.MA,C.F.CHANG,T.H.HUANG JRNL TITL STRUCTURAL ANALYSIS OF POLY-SUMO CHAIN RECOGNITION BY THE JRNL TITL 2 RNF4-SIMS DOMAIN. JRNL REF BIOCHEM.J. V. 462 53 2014 JRNL REFN ISSN 0264-6021 JRNL PMID 24844634 JRNL DOI 10.1042/BJ20140521 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 8594 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 407 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 23.2086 - 2.3549 0.99 2698 135 0.1988 0.1973 REMARK 3 2 2.3549 - 1.8695 1.00 2739 144 0.1925 0.2511 REMARK 3 3 1.8695 - 1.6332 0.99 2750 128 0.2058 0.2645 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 36.19 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.010 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) : 0.20990 REMARK 3 B22 (A**2) : 0.20990 REMARK 3 B33 (A**2) : -0.41970 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 584 REMARK 3 ANGLE : 1.087 783 REMARK 3 CHIRALITY : 0.080 85 REMARK 3 PLANARITY : 0.004 104 REMARK 3 DIHEDRAL : 15.959 229 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 17:87) REMARK 3 ORIGIN FOR THE GROUP (A): 12.8681 -5.2994 -5.3943 REMARK 3 T TENSOR REMARK 3 T11: 0.0923 T22: 0.1154 REMARK 3 T33: 0.1006 T12: 0.0160 REMARK 3 T13: -0.0003 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 2.9954 L22: 1.4740 REMARK 3 L33: 1.3692 L12: 0.0864 REMARK 3 L13: 0.5171 L23: 0.0842 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.1558 S13: -0.0247 REMARK 3 S21: 0.0424 S22: 0.0282 S23: -0.0267 REMARK 3 S31: 0.1067 S32: 0.1216 S33: 0.0001 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 4NPN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083498. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6500 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8785 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.36200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.098 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 0.1M CHES, 30% PEG 600, REMARK 280 PH 9.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.56150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.68614 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.03867 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 37.56150 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 21.68614 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.03867 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 37.56150 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 21.68614 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 11.03867 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.37228 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 22.07733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 43.37228 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 22.07733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 43.37228 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 22.07733 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: TETRAMERIC 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -37.56150 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 21.68614 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 11.03867 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 108 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 GLY A -7 REMARK 465 SER A -6 REMARK 465 HIS A -5 REMARK 465 MET A -4 REMARK 465 ALA A -3 REMARK 465 SER A -2 REMARK 465 MET A -1 REMARK 465 THR A 0 REMARK 465 GLY A 1 REMARK 465 GLY A 2 REMARK 465 GLN A 3 REMARK 465 GLN A 4 REMARK 465 MET A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 GLY A 8 REMARK 465 SER A 9 REMARK 465 GLU A 10 REMARK 465 PHE A 11 REMARK 465 THR A 12 REMARK 465 GLU A 13 REMARK 465 ASN A 14 REMARK 465 ASN A 15 REMARK 465 ASP A 16 REMARK 465 GLN A 88 REMARK 465 GLN A 89 REMARK 465 GLN A 90 REMARK 465 THR A 91 REMARK 465 GLY A 92 REMARK 465 GLY A 93 REMARK 465 LEU A 94 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BKG RELATED DB: PDB REMARK 900 LINEAR FUSION-PROTEIN OF 2 SUMO2 (WITH DELTA N11 MUTATION) REMARK 900 RELATED ID: 1WM2 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL OF HUMAN SUMO-2 WITH RESIDUES 12-89 FRGAMENT REMARK 900 RELATED ID: 1WM3 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL OF HUMAN SUMO-2 FROM RESIDUES 17-88 REMARK 900 RELATED ID: 2RPQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SUMO-2 WITH MCAF-1 DBREF 4NPN A 12 93 UNP P61956 SUMO2_HUMAN 12 93 SEQADV 4NPN GLY A -7 UNP P61956 EXPRESSION TAG SEQADV 4NPN SER A -6 UNP P61956 EXPRESSION TAG SEQADV 4NPN HIS A -5 UNP P61956 EXPRESSION TAG SEQADV 4NPN MET A -4 UNP P61956 EXPRESSION TAG SEQADV 4NPN ALA A -3 UNP P61956 EXPRESSION TAG SEQADV 4NPN SER A -2 UNP P61956 EXPRESSION TAG SEQADV 4NPN MET A -1 UNP P61956 EXPRESSION TAG SEQADV 4NPN THR A 0 UNP P61956 EXPRESSION TAG SEQADV 4NPN GLY A 1 UNP P61956 EXPRESSION TAG SEQADV 4NPN GLY A 2 UNP P61956 EXPRESSION TAG SEQADV 4NPN GLN A 3 UNP P61956 EXPRESSION TAG SEQADV 4NPN GLN A 4 UNP P61956 EXPRESSION TAG SEQADV 4NPN MET A 5 UNP P61956 EXPRESSION TAG SEQADV 4NPN GLY A 6 UNP P61956 EXPRESSION TAG SEQADV 4NPN ARG A 7 UNP P61956 EXPRESSION TAG SEQADV 4NPN GLY A 8 UNP P61956 EXPRESSION TAG SEQADV 4NPN SER A 9 UNP P61956 EXPRESSION TAG SEQADV 4NPN GLU A 10 UNP P61956 EXPRESSION TAG SEQADV 4NPN PHE A 11 UNP P61956 EXPRESSION TAG SEQADV 4NPN LEU A 94 UNP P61956 EXPRESSION TAG SEQRES 1 A 102 GLY SER HIS MET ALA SER MET THR GLY GLY GLN GLN MET SEQRES 2 A 102 GLY ARG GLY SER GLU PHE THR GLU ASN ASN ASP HIS ILE SEQRES 3 A 102 ASN LEU LYS VAL ALA GLY GLN ASP GLY SER VAL VAL GLN SEQRES 4 A 102 PHE LYS ILE LYS ARG HIS THR PRO LEU SER LYS LEU MET SEQRES 5 A 102 LYS ALA TYR CYS GLU ARG GLN GLY LEU SER MET ARG GLN SEQRES 6 A 102 ILE ARG PHE ARG PHE ASP GLY GLN PRO ILE ASN GLU THR SEQRES 7 A 102 ASP THR PRO ALA GLN LEU GLU MET GLU ASP GLU ASP THR SEQRES 8 A 102 ILE ASP VAL PHE GLN GLN GLN THR GLY GLY LEU FORMUL 2 HOH *29(H2 O) HELIX 1 1 LEU A 40 GLY A 52 1 13 SHEET 1 A 5 VAL A 29 ILE A 34 0 SHEET 2 A 5 ILE A 18 ALA A 23 -1 N ILE A 18 O ILE A 34 SHEET 3 A 5 ASP A 82 PHE A 87 1 O ILE A 84 N LYS A 21 SHEET 4 A 5 ARG A 59 PHE A 62 -1 N ARG A 61 O ASP A 85 SHEET 5 A 5 GLN A 65 PRO A 66 -1 O GLN A 65 N PHE A 62 CRYST1 75.123 75.123 33.116 90.00 90.00 120.00 H 3 9 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 0.013312 0.007685 0.000000 0.00000 SCALE2 0.000000 0.015371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030197 0.00000