PDB Short entry for 2JQZ HEADER LIGASE 15-JUN-07 2JQZ TITLE SOLUTION STRUCTURE OF THE C2 DOMAIN OF HUMAN SMURF2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE SMURF2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SMAD UBIQUITINATION REGULATORY FACTOR 2, SMAD-SPECIFIC E3 COMPND 5 UBIQUITIN LIGASE 2, HSMURF2; COMPND 6 EC: 6.3.2.-; 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: SMURF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: CODONPLUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: MODIFIED PET24D KEYWDS C2 DOMAIN, SMURF2, UBIQUITIN PROTEIN LIGASE, PHOSPHOLIPID BINDING, KEYWDS 2 LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.WIESNER,A.A.OGUNJIMI,H.WANG,D.ROTIN,F.SICHERI,J.L.WRANA,J.D.FORMAN- AUTHOR 2 KAY REVDAT 4 20-DEC-23 2JQZ 1 REMARK REVDAT 3 19-FEB-20 2JQZ 1 REMARK REVDAT 2 24-FEB-09 2JQZ 1 VERSN REVDAT 1 11-SEP-07 2JQZ 0 JRNL AUTH S.WIESNER,A.A.OGUNJIMI,H.-R.WANG,D.ROTIN,F.SICHERI, JRNL AUTH 2 J.L.WRANA,J.D.FORMAN-KAY JRNL TITL AUTOINHIBITION OF THE HECT-TYPE UBIQUITIN LIGASE SMURF2 JRNL TITL 2 THROUGH ITS C2 DOMAIN JRNL REF CELL(CAMBRIDGE,MASS.) V. 130 651 2007 JRNL REFN ISSN 0092-8674 JRNL PMID 17719543 JRNL DOI 10.1016/J.CELL.2007.06.050 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JQZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100179. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM HEPES, 200 MM SODIUM REMARK 210 CHLORIDE, 3 MM DTT, 0.03 % REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O; REMARK 210 20 MM HEPES, 200 MM SODIUM REMARK 210 CHLORIDE, 3 MM DTT, 0.03 % REMARK 210 SODIUM AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCA; 3D HNCACB; 3D HN(CO)CA; 3D REMARK 210 H(CCO)NH; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 5 TYR A 65 CE1 TYR A 65 CZ 0.103 REMARK 500 5 TYR A 65 CZ TYR A 65 CE2 -0.094 REMARK 500 16 TYR A 65 CE1 TYR A 65 CZ 0.118 REMARK 500 16 TYR A 65 CZ TYR A 65 CE2 -0.106 REMARK 500 17 TYR A 65 CE1 TYR A 65 CZ 0.116 REMARK 500 17 TYR A 65 CZ TYR A 65 CE2 -0.113 REMARK 500 20 TYR A 112 CZ TYR A 112 CE2 0.089 REMARK 500 REMARK 500 REMARK: NULL 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 1 LYS A 27 -84.23 59.60 REMARK 500 1 PHE A 30 -5.90 63.85 REMARK 500 1 ASP A 51 162.09 -48.77 REMARK 500 1 ASN A 55 88.38 17.22 REMARK 500 1 ASP A 58 79.62 -161.31 REMARK 500 1 LYS A 71 -83.12 56.88 REMARK 500 1 LYS A 88 172.12 64.53 REMARK 500 1 GLN A 89 61.30 66.23 REMARK 500 1 LEU A 94 -80.66 -124.06 REMARK 500 1 TYR A 112 135.62 -175.47 REMARK 500 1 ASN A 125 79.03 55.40 REMARK 500 1 THR A 127 52.85 -108.35 REMARK 500 1 ARG A 129 4.43 167.90 REMARK 500 2 LYS A 27 -79.24 60.07 REMARK 500 2 PHE A 29 -81.49 -44.15 REMARK 500 2 ASP A 34 78.51 -112.78 REMARK 500 2 ASP A 42 86.10 -65.13 REMARK 500 2 ASP A 51 158.90 -48.98 REMARK 500 2 ASN A 55 89.75 18.11 REMARK 500 2 ASP A 58 77.11 -160.16 REMARK 500 2 TRP A 61 -31.53 -131.89 REMARK 500 2 LYS A 71 -83.89 53.95 REMARK 500 2 SER A 72 40.45 -141.70 REMARK 500 2 LYS A 87 -6.87 -58.30 REMARK 500 2 LYS A 88 171.78 70.31 REMARK 500 2 GLN A 89 -169.64 60.81 REMARK 500 2 LEU A 94 -66.41 -130.55 REMARK 500 2 TYR A 112 98.98 60.52 REMARK 500 2 ASN A 125 95.18 58.18 REMARK 500 2 ASP A 126 75.67 -106.78 REMARK 500 2 ARG A 129 6.30 168.08 REMARK 500 3 ASN A 23 66.82 37.89 REMARK 500 3 LYS A 27 -79.52 61.06 REMARK 500 3 ASP A 34 77.33 -112.56 REMARK 500 3 ASP A 42 86.18 -65.35 REMARK 500 3 ASP A 51 160.38 -49.20 REMARK 500 3 ASN A 55 85.45 17.75 REMARK 500 3 ASP A 58 81.41 -160.07 REMARK 500 3 PRO A 59 -164.90 -79.80 REMARK 500 3 TRP A 61 -39.36 -131.88 REMARK 500 3 LYS A 71 -85.72 54.50 REMARK 500 3 LYS A 88 -163.30 179.59 REMARK 500 3 LEU A 94 50.90 -148.01 REMARK 500 3 TYR A 112 89.85 179.21 REMARK 500 3 ASP A 126 62.87 -158.77 REMARK 500 3 THR A 127 74.17 49.71 REMARK 500 3 ARG A 129 107.11 163.57 REMARK 500 4 ASN A 23 74.36 41.05 REMARK 500 4 LYS A 27 -83.39 51.30 REMARK 500 4 ASP A 42 86.10 -66.16 REMARK 500 REMARK 500 THIS ENTRY HAS 312 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 TYR A 112 0.07 SIDE CHAIN REMARK 500 5 TYR A 65 0.06 SIDE CHAIN REMARK 500 10 TYR A 112 0.08 SIDE CHAIN REMARK 500 16 TYR A 65 0.07 SIDE CHAIN REMARK 500 17 TYR A 65 0.05 SIDE CHAIN REMARK 500 20 TYR A 112 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZVD RELATED DB: PDB REMARK 900 SMURF2 HECT DOMAIN REMARK 900 RELATED ID: 15306 RELATED DB: BMRB DBREF 2JQZ A 10 140 UNP Q9HAU4 SMUF2_HUMAN 10 140 SEQRES 1 A 131 GLY PRO VAL LYS LEU ARG LEU THR VAL LEU CYS ALA LYS SEQRES 2 A 131 ASN LEU VAL LYS LYS ASP PHE PHE ARG LEU PRO ASP PRO SEQRES 3 A 131 PHE ALA LYS VAL VAL VAL ASP GLY SER GLY GLN CYS HIS SEQRES 4 A 131 SER THR ASP THR VAL LYS ASN THR LEU ASP PRO LYS TRP SEQRES 5 A 131 ASN GLN HIS TYR ASP LEU TYR ILE GLY LYS SER ASP SER SEQRES 6 A 131 VAL THR ILE SER VAL TRP ASN HIS LYS LYS ILE HIS LYS SEQRES 7 A 131 LYS GLN GLY ALA GLY PHE LEU GLY CYS VAL ARG LEU LEU SEQRES 8 A 131 SER ASN ALA ILE ASN ARG LEU LYS ASP THR GLY TYR GLN SEQRES 9 A 131 ARG LEU ASP LEU CYS LYS LEU GLY PRO ASN ASP ASN ASP SEQRES 10 A 131 THR VAL ARG GLY GLN ILE VAL VAL SER LEU GLN SER ARG SEQRES 11 A 131 ASP HELIX 1 1 HIS A 82 LYS A 88 1 7 HELIX 2 2 LEU A 100 GLY A 111 1 12 SHEET 1 A 4 LYS A 60 ILE A 69 0 SHEET 2 A 4 VAL A 12 LYS A 22 -1 N VAL A 18 O GLN A 63 SHEET 3 A 4 GLN A 131 SER A 138 -1 O VAL A 133 N CYS A 20 SHEET 4 A 4 GLN A 113 LEU A 115 -1 N GLN A 113 O VAL A 134 SHEET 1 B 4 HIS A 48 THR A 50 0 SHEET 2 B 4 PRO A 35 VAL A 41 -1 N VAL A 39 O HIS A 48 SHEET 3 B 4 VAL A 75 ASN A 81 -1 O SER A 78 N LYS A 38 SHEET 4 B 4 PHE A 93 LEU A 99 -1 O VAL A 97 N ILE A 77 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000