HEADER PROTEIN TRANSPORT 07-OCT-04 1WR0 TITLE STRUCTURAL CHARACTERIZATION OF THE MIT DOMAIN FROM HUMAN VPS4B COMPND MOL_ID: 1; COMPND 2 MOLECULE: SKD1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MIT DOMAIN; COMPND 5 SYNONYM: VACUOLAR SORTING PROTEIN 4B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRESAT KEYWDS VPS4B, SKD1, MIT DOMAIN, ESCORT, MVB, SNPS, PROTEIN TRANSPORT, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.TAKASU,J.G.JEE,A.OHNO,N.GODA,K.FUJIWARA,H.TOCHIO,M.SHIRAKAWA, AUTHOR 2 H.HIROAKI,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 02-MAR-22 1WR0 1 REMARK SEQADV ATOM REVDAT 3 24-FEB-09 1WR0 1 VERSN REVDAT 2 09-OCT-07 1WR0 1 REMARK AUTHOR KEYWDS REVDAT 1 02-AUG-05 1WR0 0 JRNL AUTH H.TAKASU,J.G.JEE,A.OHNO,N.GODA,K.FUJIWARA,H.TOCHIO, JRNL AUTH 2 M.SHIRAKAWA,H.HIROAKI JRNL TITL STRUCTURAL CHARACTERIZATION OF THE MIT DOMAIN FROM HUMAN JRNL TITL 2 VPS4B JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 334 460 2005 JRNL REFN ISSN 0006-291X JRNL PMID 16018968 JRNL DOI 10.1016/J.BBRC.2005.06.110 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 7.0 REMARK 3 AUTHORS : PEARLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1539 RESTRAINTS, 1471 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 68 REMARK 3 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1WR0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000023897. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NACL 50MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM PROTEIN U-15N; 20MM TRIS REMARK 210 BUFFER; 50MM NACL; 95% H2O, 5% REMARK 210 D2O; 1MM DTT; 1MM PROTEIN U-15N, REMARK 210 13C; 20MM TRIS BUFFER; 50MM NACL; REMARK 210 95% H2O, 5% D2O; 1MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, SPARKY 3.110, CYANA REMARK 210 2.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 94 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 : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 8 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES 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 ASP A 3 52.23 38.72 REMARK 500 1 HIS A 4 -22.44 61.28 REMARK 500 1 TYR A 31 55.90 36.17 REMARK 500 1 GLU A 32 -75.16 -130.85 REMARK 500 1 ASP A 56 -89.45 48.86 REMARK 500 1 LEU A 80 107.20 -38.54 REMARK 500 2 MET A 5 -9.67 49.12 REMARK 500 2 SER A 7 -2.34 60.93 REMARK 500 2 TYR A 31 54.35 35.97 REMARK 500 2 GLU A 32 -71.42 -134.79 REMARK 500 3 SER A 6 -33.87 62.36 REMARK 500 3 TYR A 31 55.09 34.37 REMARK 500 3 GLU A 32 -76.12 -132.40 REMARK 500 3 GLU A 52 -147.91 -136.40 REMARK 500 3 ALA A 53 178.81 66.25 REMARK 500 3 ASP A 56 -65.47 -125.17 REMARK 500 4 MET A 5 -37.47 66.76 REMARK 500 4 TYR A 31 54.98 32.95 REMARK 500 4 GLU A 32 -78.82 -130.14 REMARK 500 4 ASP A 56 -91.38 39.87 REMARK 500 5 SER A 2 -11.15 -143.04 REMARK 500 5 MET A 5 -73.33 55.41 REMARK 500 5 SER A 7 -28.31 67.37 REMARK 500 5 TYR A 31 71.32 -63.56 REMARK 500 5 GLU A 32 -67.91 -160.15 REMARK 500 5 GLU A 52 38.12 -141.49 REMARK 500 5 LEU A 80 105.86 -34.93 REMARK 500 6 TYR A 31 54.13 35.00 REMARK 500 6 GLU A 32 -79.26 -132.84 REMARK 500 7 TYR A 31 56.56 35.85 REMARK 500 7 GLU A 32 -57.48 -128.95 REMARK 500 7 GLU A 52 32.80 -146.56 REMARK 500 7 ASP A 56 -83.69 -80.53 REMARK 500 7 LEU A 80 104.89 -41.77 REMARK 500 8 MET A 5 -1.19 48.20 REMARK 500 8 TYR A 31 65.65 25.21 REMARK 500 8 GLU A 32 -79.08 -141.80 REMARK 500 8 ALA A 53 109.11 -49.16 REMARK 500 9 TYR A 31 62.90 28.58 REMARK 500 9 GLU A 32 -72.73 -139.11 REMARK 500 9 ASP A 56 -70.07 -75.36 REMARK 500 10 HIS A 4 -30.46 -150.46 REMARK 500 10 SER A 6 -24.39 62.79 REMARK 500 10 TYR A 31 54.88 35.86 REMARK 500 10 GLU A 32 -75.63 -131.54 REMARK 500 10 ASP A 56 -76.94 -103.50 REMARK 500 11 MET A 5 31.08 -76.74 REMARK 500 11 TYR A 31 54.97 35.16 REMARK 500 11 GLU A 32 -78.96 -132.94 REMARK 500 11 ASP A 56 -70.31 -68.98 REMARK 500 REMARK 500 THIS ENTRY HAS 88 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 5 ARG A 72 0.08 SIDE CHAIN REMARK 500 16 ARG A 72 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: AR_001000797.1 RELATED DB: TARGETDB DBREF 1WR0 A 5 81 UNP O75351 VPS4B_HUMAN 1 77 SEQADV 1WR0 GLY A 1 UNP O75351 EXPRESSION TAG SEQADV 1WR0 SER A 2 UNP O75351 EXPRESSION TAG SEQADV 1WR0 ASP A 3 UNP O75351 EXPRESSION TAG SEQADV 1WR0 HIS A 4 UNP O75351 EXPRESSION TAG SEQRES 1 A 81 GLY SER ASP HIS MET SER SER THR SER PRO ASN LEU GLN SEQRES 2 A 81 LYS ALA ILE ASP LEU ALA SER LYS ALA ALA GLN GLU ASP SEQRES 3 A 81 LYS ALA GLY ASN TYR GLU GLU ALA LEU GLN LEU TYR GLN SEQRES 4 A 81 HIS ALA VAL GLN TYR PHE LEU HIS VAL VAL LYS TYR GLU SEQRES 5 A 81 ALA GLN GLY ASP LYS ALA LYS GLN SER ILE ARG ALA LYS SEQRES 6 A 81 CYS THR GLU TYR LEU ASP ARG ALA GLU LYS LEU LYS GLU SEQRES 7 A 81 TYR LEU LYS HELIX 1 1 SER A 9 ALA A 28 1 20 HELIX 2 2 GLU A 33 GLU A 52 1 20 HELIX 3 3 GLY A 55 ALA A 58 5 4 HELIX 4 4 LYS A 59 LYS A 77 1 19 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 MODEL 1