PDB Short entry for 2CPT HEADER PROTEIN TRANSPORT 19-MAY-05 2CPT TITLE SOLUTION STRUCTURE OF MIT DOMAIN FROM HUMAN SKD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR SORTING PROTEIN 4B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MIT DOMAIN; COMPND 5 SYNONYM: SKD1 PROTEIN; 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 GENE: VPS4B, SKD1, VPS42; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040607-08; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS MIT, SKD1, HELIX BUNDLE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SUETAKE,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2CPT 1 REMARK SEQADV REVDAT 2 24-FEB-09 2CPT 1 VERSN REVDAT 1 19-NOV-05 2CPT 0 JRNL AUTH T.SUETAKE,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF MIT DOMAIN FROM HUMAN SKD1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CPT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024486. 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 : 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.11MM 13C, 15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL; 100MM NACL; 1MM REMARK 210 D10-DTT; 0.02% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.927, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATION, TARGET REMARK 210 FUNCTION 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: 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 SER A 5 99.81 -45.74 REMARK 500 1 SER A 6 120.74 -172.11 REMARK 500 1 SER A 10 104.55 -57.71 REMARK 500 1 GLU A 55 37.76 -83.16 REMARK 500 1 ALA A 56 -177.72 -65.28 REMARK 500 1 GLN A 57 -63.87 -127.97 REMARK 500 1 ASP A 59 -38.55 -38.94 REMARK 500 1 GLU A 77 -39.73 -39.28 REMARK 500 1 LYS A 89 137.94 -37.55 REMARK 500 1 GLU A 104 151.70 -35.17 REMARK 500 1 LYS A 105 165.46 -43.76 REMARK 500 1 ASN A 107 161.10 -43.85 REMARK 500 1 SER A 116 92.66 -50.11 REMARK 500 2 SER A 6 122.27 -174.08 REMARK 500 2 SER A 9 42.26 -92.13 REMARK 500 2 SER A 12 155.77 -40.78 REMARK 500 2 HIS A 50 -39.89 -39.84 REMARK 500 2 GLU A 55 35.45 -84.00 REMARK 500 2 GLN A 57 -72.02 -100.84 REMARK 500 2 GLN A 63 -37.17 -37.75 REMARK 500 2 LEU A 79 -32.56 -38.10 REMARK 500 2 LYS A 88 94.19 -52.46 REMARK 500 2 ALA A 90 105.94 -51.15 REMARK 500 2 VAL A 94 76.90 -113.96 REMARK 500 2 PRO A 99 -166.90 -69.82 REMARK 500 2 ALA A 102 105.40 -50.84 REMARK 500 2 PRO A 114 -178.40 -69.70 REMARK 500 3 SER A 3 42.08 39.37 REMARK 500 3 SER A 6 98.57 -61.23 REMARK 500 3 GLU A 55 39.67 -83.10 REMARK 500 3 ALA A 56 161.37 -47.17 REMARK 500 3 GLU A 87 173.49 -49.77 REMARK 500 3 LYS A 89 97.69 -38.16 REMARK 500 3 GLN A 91 75.91 -66.68 REMARK 500 3 VAL A 94 135.64 -37.88 REMARK 500 3 GLU A 96 91.32 -68.47 REMARK 500 3 PRO A 99 -175.35 -69.72 REMARK 500 3 ASP A 110 136.19 -171.74 REMARK 500 3 PRO A 114 -177.64 -69.78 REMARK 500 4 SER A 3 152.87 -47.75 REMARK 500 4 GLU A 55 38.88 -82.65 REMARK 500 4 LYS A 92 144.90 -38.92 REMARK 500 5 SER A 12 154.40 -47.22 REMARK 500 5 ALA A 56 155.99 -41.86 REMARK 500 5 GLN A 57 -64.01 -108.77 REMARK 500 5 GLN A 91 98.06 -60.96 REMARK 500 6 GLU A 55 40.01 -82.21 REMARK 500 6 GLN A 57 -67.21 -125.29 REMARK 500 6 LYS A 60 -70.43 -58.27 REMARK 500 6 LEU A 79 -30.59 -36.06 REMARK 500 REMARK 500 THIS ENTRY HAS 189 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSS001000811.1 RELATED DB: TARGETDB DBREF 2CPT A 8 111 UNP O75351 VPS4B_HUMAN 1 104 SEQADV 2CPT GLY A 1 UNP O75351 CLONING ARTIFACT SEQADV 2CPT SER A 2 UNP O75351 CLONING ARTIFACT SEQADV 2CPT SER A 3 UNP O75351 CLONING ARTIFACT SEQADV 2CPT GLY A 4 UNP O75351 CLONING ARTIFACT SEQADV 2CPT SER A 5 UNP O75351 CLONING ARTIFACT SEQADV 2CPT SER A 6 UNP O75351 CLONING ARTIFACT SEQADV 2CPT GLY A 7 UNP O75351 CLONING ARTIFACT SEQADV 2CPT SER A 112 UNP O75351 CLONING ARTIFACT SEQADV 2CPT GLY A 113 UNP O75351 CLONING ARTIFACT SEQADV 2CPT PRO A 114 UNP O75351 CLONING ARTIFACT SEQADV 2CPT SER A 115 UNP O75351 CLONING ARTIFACT SEQADV 2CPT SER A 116 UNP O75351 CLONING ARTIFACT SEQADV 2CPT GLY A 117 UNP O75351 CLONING ARTIFACT SEQRES 1 A 117 GLY SER SER GLY SER SER GLY MET SER SER THR SER PRO SEQRES 2 A 117 ASN LEU GLN LYS ALA ILE ASP LEU ALA SER LYS ALA ALA SEQRES 3 A 117 GLN GLU ASP LYS ALA GLY ASN TYR GLU GLU ALA LEU GLN SEQRES 4 A 117 LEU TYR GLN HIS ALA VAL GLN TYR PHE LEU HIS VAL VAL SEQRES 5 A 117 LYS TYR GLU ALA GLN GLY ASP LYS ALA LYS GLN SER ILE SEQRES 6 A 117 ARG ALA LYS CYS THR GLU TYR LEU ASP ARG ALA GLU LYS SEQRES 7 A 117 LEU LYS GLU TYR LEU LYS ASN LYS GLU LYS LYS ALA GLN SEQRES 8 A 117 LYS PRO VAL LYS GLU GLY GLN PRO SER PRO ALA ASP GLU SEQRES 9 A 117 LYS GLY ASN ASP SER ASP GLY SER GLY PRO SER SER GLY HELIX 1 1 SER A 12 GLY A 32 1 21 HELIX 2 2 ASN A 33 TYR A 54 1 22 HELIX 3 3 GLY A 58 GLU A 87 1 30 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