HEADER PROTEIN TRANSPORT 09-DEC-04 1Y7N
TITLE SOLUTION STRUCTURE OF THE SECOND PDZ DOMAIN OF THE HUMAN NEURONAL
TITLE 2 ADAPTOR X11ALPHA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A MEMBER
COMPND 3 1;
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: SECOND PDZ DOMAIN;
COMPND 6 SYNONYM: NEURON-SPECIFIC X11 PROTEIN, NEURONAL MUNC18-1-INTERACTING
COMPND 7 PROTEIN 1, MINT-1, ADAPTER PROTEIN X11ALPHA;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 TISSUE: BRAIN;
SOURCE 6 GENE: APBA1;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) *RP;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET3H
KEYWDS COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE, NEURONAL ADAPTOR, PROTEIN
KEYWDS 2 TRANSPORT
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR A.E.DUQUESNE,M.DE RUIJTER,J.BROUWER,J.W.DRIJFHOUT,S.B.NABUURS,
AUTHOR 2 C.A.E.M.SPRONK,G.W.VUISTER,M.UBBINK,G.W.CANTERS
REVDAT 3 02-MAR-22 1Y7N 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1Y7N 1 VERSN
REVDAT 1 22-NOV-05 1Y7N 0
JRNL AUTH A.E.DUQUESNE,M.DE RUIJTER,J.BROUWER,J.W.DRIJFHOUT,
JRNL AUTH 2 S.B.NABUURS,C.A.E.M.SPRONK,G.W.VUISTER,M.UBBINK,G.W.CANTERS
JRNL TITL SOLUTION STRUCTURE OF THE SECOND PDZ DOMAIN OF THE NEURONAL
JRNL TITL 2 ADAPTOR X11ALPHA AND ITS INTERACTION WITH THE C-TERMINAL
JRNL TITL 3 PEPTIDE OF THE HUMAN COPPER CHAPERONE FOR SUPEROXIDE
JRNL TITL 4 DISMUTASE
JRNL REF J.BIOMOL.NMR V. 32 209 2005
JRNL REFN ISSN 0925-2738
JRNL PMID 16132821
JRNL DOI 10.1007/S10858-005-7333-1
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 2002 RELEASE, X-PLOR 2.9.6
REMARK 3 AUTHORS : F. DELAGLIO, S. GRZESIEK, G. W. VUISTER, G. ZHU,
REMARK 3 J. PFEIFER AND A. BAX (NMRPIPE), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE FINAL STRUCTURE CALCULATIONS WITH CYANA WERE STARTED FROM 100
REMARK 3 CONFORMERS WITH RANDOM TORSION ANGLE VALUES. SIMULATED ANNEALING
REMARK 3 WITH 10,000 TIME STEPS PER CONFORMER WAS DONE USING THE DYANA
REMARK 3 TORSION ANGLE DYNAMICS ALGORITHM. USING THE FORMATCONVERTER,
REMARK 3 DEVELOPED AS PART OF THE COLLABORATIVE COMPUTING PROJECT FOR THE
REMARK 3 NMR COMMUNITY (CCPN), THE DISTANCE AND DIHEDRAL ANGLE RESTRAINTS
REMARK 3 WERE CONVERTED TO THE X-PLOR RESTRAINT FORMAT. SUBSEQUENTLY THE
REMARK 3 100 GENERATED STRUCTURES WERE REFINED USING A SH
REMARK 3 RT RESTRAINED MOLECULAR DYNAMICS SIMULATION IN EXPLICIT SOLVENT IN
REMARK 3 THE PROGRAM XPLOR-NIH. OF THESE, THE 20 LOWEST ENERGY STRUCTURES
REMARK 3 WERE SELECTED TO FORM THE FINAL ENSEMBLE.
REMARK 4
REMARK 4 1Y7N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-05.
REMARK 100 THE DEPOSITION ID IS D_1000031218.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 290
REMARK 210 PH : 6.7
REMARK 210 IONIC STRENGTH : 10MM
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 1.2MM PDZ2A U-15N,13C; 10MM
REMARK 210 SODIUM PHOSPHATE BUFFER; PH 6.7;
REMARK 210 95% H2O; 5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CARA 1.1.8, CYANA 1.0, VNMR
REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR
REMARK 210 DYNAMICS SIMULATION, TORSION
REMARK 210 ANGLE DYNAMICS, DISTANCE AND
REMARK 210 DIHEDRAL ANGLE RESTRAINTS
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-20
REMARK 465 RES C SSSEQI
REMARK 465 HIS A 1
REMARK 465 HIS A 2
REMARK 465 HIS A 3
REMARK 465 HIS A 4
REMARK 465 HIS A 5
REMARK 465 LEU A 6
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: 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 THR A 8 77.13 61.22
REMARK 500 1 PRO A 88 28.71 -70.27
REMARK 500 2 PRO A 88 31.31 -74.71
REMARK 500 3 ASP A 21 -175.46 -171.71
REMARK 500 3 PRO A 88 35.64 -74.30
REMARK 500 4 PRO A 88 31.49 -72.74
REMARK 500 5 MET A 9 -46.24 -173.95
REMARK 500 5 PRO A 88 32.42 -68.20
REMARK 500 6 GLN A 25 -168.42 -121.63
REMARK 500 6 PRO A 88 29.50 -71.04
REMARK 500 6 ALA A 89 -2.36 71.00
REMARK 500 7 ASN A 32 12.80 59.86
REMARK 500 7 PRO A 88 29.83 -75.98
REMARK 500 8 THR A 8 93.69 83.29
REMARK 500 8 ASN A 32 -1.14 64.20
REMARK 500 8 PRO A 88 27.52 -73.77
REMARK 500 9 ASN A 11 88.26 63.22
REMARK 500 9 PRO A 88 30.27 -74.84
REMARK 500 10 GLN A 25 -164.46 57.05
REMARK 500 10 PRO A 88 26.26 -69.71
REMARK 500 10 ALA A 89 -1.27 74.86
REMARK 500 11 GLU A 81 108.78 -59.11
REMARK 500 12 THR A 8 140.11 64.93
REMARK 500 12 ASN A 11 92.09 62.19
REMARK 500 12 ASP A 21 -176.89 -176.73
REMARK 500 12 PRO A 88 29.58 -71.29
REMARK 500 13 ASP A 21 -170.49 -173.10
REMARK 500 13 PRO A 88 38.76 -70.79
REMARK 500 14 ASN A 32 11.97 59.39
REMARK 500 14 PRO A 88 24.33 -71.42
REMARK 500 15 GLN A 25 -153.58 54.09
REMARK 500 15 PRO A 88 29.67 -75.51
REMARK 500 16 ASN A 11 86.79 68.91
REMARK 500 16 PRO A 88 26.64 -70.69
REMARK 500 17 ASN A 59 -21.18 73.38
REMARK 500 17 PRO A 88 22.33 -72.94
REMARK 500 18 GLN A 25 -157.27 -97.07
REMARK 500 18 PRO A 88 24.91 -72.10
REMARK 500 19 ASN A 59 -2.72 69.43
REMARK 500 19 PRO A 88 29.68 -78.33
REMARK 500 20 ASN A 11 89.88 63.48
REMARK 500 20 ASN A 59 -18.66 70.84
REMARK 500 20 PRO A 88 30.05 -74.48
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 1 ARG A 19 0.08 SIDE CHAIN
REMARK 500 3 ARG A 18 0.09 SIDE CHAIN
REMARK 500 5 ARG A 19 0.07 SIDE CHAIN
REMARK 500 5 ARG A 54 0.08 SIDE CHAIN
REMARK 500 8 ARG A 19 0.11 SIDE CHAIN
REMARK 500 9 ARG A 50 0.08 SIDE CHAIN
REMARK 500 10 ARG A 23 0.13 SIDE CHAIN
REMARK 500 11 ARG A 19 0.09 SIDE CHAIN
REMARK 500 12 ARG A 40 0.08 SIDE CHAIN
REMARK 500 13 ARG A 50 0.08 SIDE CHAIN
REMARK 500 13 ARG A 54 0.11 SIDE CHAIN
REMARK 500 14 ARG A 23 0.08 SIDE CHAIN
REMARK 500 14 ARG A 46 0.09 SIDE CHAIN
REMARK 500 15 ARG A 54 0.08 SIDE CHAIN
REMARK 500 16 ARG A 18 0.12 SIDE CHAIN
REMARK 500 17 ARG A 19 0.07 SIDE CHAIN
REMARK 500 18 ARG A 18 0.08 SIDE CHAIN
REMARK 500 19 ARG A 18 0.08 SIDE CHAIN
REMARK 500 19 ARG A 46 0.10 SIDE CHAIN
REMARK 500 20 ARG A 19 0.09 SIDE CHAIN
REMARK 500 20 ARG A 50 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1Y7N A 12 90 UNP Q02410 APBA1_HUMAN 745 823
SEQADV 1Y7N HIS A 1 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N HIS A 2 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N HIS A 3 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N HIS A 4 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N HIS A 5 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N LEU A 6 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N GLU A 7 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N THR A 8 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N MET A 9 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N GLY A 10 UNP Q02410 EXPRESSION TAG
SEQADV 1Y7N ASN A 11 UNP Q02410 EXPRESSION TAG
SEQRES 1 A 90 HIS HIS HIS HIS HIS LEU GLU THR MET GLY ASN VAL THR
SEQRES 2 A 90 THR VAL LEU ILE ARG ARG PRO ASP LEU ARG TYR GLN LEU
SEQRES 3 A 90 GLY PHE SER VAL GLN ASN GLY ILE ILE CYS SER LEU MET
SEQRES 4 A 90 ARG GLY GLY ILE ALA GLU ARG GLY GLY VAL ARG VAL GLY
SEQRES 5 A 90 HIS ARG ILE ILE GLU ILE ASN GLY GLN SER VAL VAL ALA
SEQRES 6 A 90 THR PRO HIS GLU LYS ILE VAL HIS ILE LEU SER ASN ALA
SEQRES 7 A 90 VAL GLY GLU ILE HIS MET LYS THR MET PRO ALA ALA
HELIX 1 1 GLY A 42 GLY A 48 1 7
HELIX 2 2 PRO A 67 ALA A 78 1 12
SHEET 1 A 4 THR A 13 ARG A 19 0
SHEET 2 A 4 GLY A 80 MET A 87 -1 O THR A 86 N THR A 13
SHEET 3 A 4 ARG A 54 ILE A 58 -1 N ILE A 56 O LYS A 85
SHEET 4 A 4 GLN A 61 SER A 62 -1 O GLN A 61 N ILE A 58
SHEET 1 B 2 PHE A 28 GLN A 31 0
SHEET 2 B 2 ILE A 34 LEU A 38 -1 O CYS A 36 N SER A 29
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
(ATOM LINES ARE NOT SHOWN.)
END
