PDB Short entry for 1KMD HEADER ENDOCYTOSIS/EXOCYTOSIS 14-DEC-01 1KMD TITLE SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR MORPHOGENESIS PROTEIN VAM7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PX DOMAIN, RESIDUES 8-124; COMPND 5 SYNONYM: VAM7P; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-KG KEYWDS PX DOMAIN, VAM7P, PHOSPHOINOSITIDE BINDING, ENDOCYTOSIS-EXOCYTOSIS KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.LU,J.GARCIA,I.DULUBOVA,T.C.SUDHOF,J.RIZO REVDAT 3 23-FEB-22 1KMD 1 REMARK REVDAT 2 24-FEB-09 1KMD 1 VERSN REVDAT 1 12-JUN-02 1KMD 0 JRNL AUTH J.LU,J.GARCIA,I.DULUBOVA,T.C.SUDHOF,J.RIZO JRNL TITL SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN. JRNL REF BIOCHEMISTRY V. 41 5956 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11993989 JRNL DOI 10.1021/BI020050B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.8, CNS 1.0 REMARK 3 AUTHORS : DELAGLIO, F. ET AL. (NMRPIPE), BRUNGER, A.T. ET REMARK 3 AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1443 RESTRAINTS, 1193 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 152 DIHEDRAL ANGLE RESTRAINTS, 98 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1KMD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015106. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 20MM MES REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5MM VAM7P PX DOMAIN U-15N,20MM REMARK 210 MES BUFFER; 0.5MM VAM7P PX REMARK 210 DOMAIN U-15N, 13C, 20MM MES REMARK 210 BUFFER; 0.5MM VAM7P PX DOMAIN U- REMARK 210 15N, 20MM MES BUFFER; 0.5MM REMARK 210 VAM7P PX DOMAIN 10%-13C, 20MM REMARK 210 MES BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, NMRVIEW 4.1.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE MINIMAL NOE REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 18 27.76 -144.25 REMARK 500 1 LYS A 36 -176.56 167.70 REMARK 500 1 LYS A 49 -73.96 -63.11 REMARK 500 1 PRO A 61 34.05 -88.50 REMARK 500 1 VAL A 70 -78.81 -81.43 REMARK 500 1 LEU A 71 39.40 -156.32 REMARK 500 1 ARG A 103 -62.28 -133.33 REMARK 500 1 LEU A 120 38.06 -92.35 REMARK 500 1 SER A 121 -168.36 -74.23 REMARK 500 2 ARG A 14 98.88 -65.10 REMARK 500 2 ASP A 18 25.62 -142.69 REMARK 500 2 LYS A 36 -179.13 165.52 REMARK 500 2 LYS A 49 -71.48 -55.09 REMARK 500 2 VAL A 70 -79.41 -77.37 REMARK 500 2 ASN A 101 52.54 -90.48 REMARK 500 2 ARG A 103 -67.45 -122.84 REMARK 500 2 LEU A 120 38.76 -91.76 REMARK 500 3 LYS A 36 -178.34 136.16 REMARK 500 3 LYS A 49 -72.80 -62.09 REMARK 500 3 PRO A 61 35.11 -88.61 REMARK 500 3 VAL A 70 -79.16 -103.20 REMARK 500 3 LEU A 71 57.95 -107.11 REMARK 500 3 LEU A 120 38.15 -92.30 REMARK 500 3 SER A 121 -163.62 -105.40 REMARK 500 4 LYS A 36 -179.41 166.59 REMARK 500 4 LYS A 49 -70.27 -56.17 REMARK 500 4 PRO A 61 34.95 -86.09 REMARK 500 4 VAL A 70 -78.98 -98.17 REMARK 500 4 ARG A 73 13.44 -141.67 REMARK 500 4 ASN A 101 57.43 -95.41 REMARK 500 4 LEU A 120 38.59 -92.03 REMARK 500 5 LYS A 36 -178.37 167.86 REMARK 500 5 LYS A 49 -72.51 -55.45 REMARK 500 5 PRO A 61 33.94 -85.52 REMARK 500 5 VAL A 70 -79.47 -67.37 REMARK 500 5 LEU A 71 70.16 -114.33 REMARK 500 5 ASN A 101 52.25 -94.17 REMARK 500 5 LEU A 120 40.45 -93.92 REMARK 500 6 ASP A 18 26.58 -155.42 REMARK 500 6 LYS A 36 177.40 169.18 REMARK 500 6 LYS A 49 -72.31 -52.54 REMARK 500 6 GLU A 66 -167.16 -74.73 REMARK 500 6 VAL A 70 -79.16 -124.35 REMARK 500 6 LEU A 71 45.52 -166.70 REMARK 500 6 ASP A 80 33.67 -98.90 REMARK 500 6 ARG A 103 -50.53 -128.64 REMARK 500 6 LEU A 120 37.48 -90.66 REMARK 500 6 SER A 121 176.40 57.11 REMARK 500 7 LYS A 36 -178.30 168.30 REMARK 500 7 PRO A 61 32.58 -87.97 REMARK 500 REMARK 500 THIS ENTRY HAS 149 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1KMD A 8 124 UNP P32912 VAM7_YEAST 8 124 SEQRES 1 A 117 LYS MET SER GLU LYS LEU ARG ILE LYS VAL ASP ASP VAL SEQRES 2 A 117 LYS ILE ASN PRO LYS TYR VAL LEU TYR GLY VAL SER THR SEQRES 3 A 117 PRO ASN LYS ARG LEU TYR LYS ARG TYR SER GLU PHE TRP SEQRES 4 A 117 LYS LEU LYS THR ARG LEU GLU ARG ASP VAL GLY SER THR SEQRES 5 A 117 ILE PRO TYR ASP PHE PRO GLU LYS PRO GLY VAL LEU ASP SEQRES 6 A 117 ARG ARG TRP GLN ARG ARG TYR ASP ASP PRO GLU MET ILE SEQRES 7 A 117 ASP GLU ARG ARG ILE GLY LEU GLU ARG PHE LEU ASN GLU SEQRES 8 A 117 LEU TYR ASN ASP ARG PHE ASP SER ARG TRP ARG ASP THR SEQRES 9 A 117 LYS ILE ALA GLN ASP PHE LEU GLN LEU SER LYS PRO ASN HELIX 1 1 ARG A 41 GLY A 57 1 17 HELIX 2 2 ASP A 81 ASN A 101 1 21 HELIX 3 3 SER A 106 THR A 111 1 6 HELIX 4 4 THR A 111 LEU A 118 1 8 SHEET 1 A 3 LEU A 38 LYS A 40 0 SHEET 2 A 3 VAL A 27 SER A 32 -1 N VAL A 31 O LEU A 38 SHEET 3 A 3 LYS A 16 VAL A 17 -1 N LYS A 16 O SER A 32 SHEET 1 B 3 LEU A 38 LYS A 40 0 SHEET 2 B 3 VAL A 27 SER A 32 -1 N VAL A 31 O LEU A 38 SHEET 3 B 3 LYS A 21 ILE A 22 -1 N LYS A 21 O LEU A 28 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