Header list of 1y8f.pdb file
Complete list - r 2 2 Bytes
HEADER ENDOCYTOSIS/EXOCYTOSIS,SIGNALING PROTEIN12-DEC-04 1Y8F
TITLE SOLUTION STRUCTURE OF THE MUNC13-1 C1-DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UNC-13 HOMOLOG A;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: C1-DOMAIN (RESIDUES 567-616);
COMPND 5 SYNONYM: MUNC13-1;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: NORWAY RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 GENE: MUNC13-1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-KG
KEYWDS CYSTEINE-RICH DOMAIN, C1-DOMAIN, ZINC-BINDING DOMAIN,
KEYWDS 2 ENDOCYTOSIS/EXOCYTOSIS, SIGNALING PROTEIN COMPLEX, ENDOCYTOSIS-
KEYWDS 3 EXOCYTOSIS
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR N.SHEN,O.GURYEV,J.RIZO
REVDAT 3 02-MAR-22 1Y8F 1 REMARK SEQADV LINK
REVDAT 2 24-FEB-09 1Y8F 1 VERSN
REVDAT 1 12-APR-05 1Y8F 0
JRNL AUTH N.SHEN,O.GURYEV,J.RIZO
JRNL TITL INTRAMOLECULAR OCCLUSION OF THE DIACYLGLYCEROL-BINDING SITE
JRNL TITL 2 IN THE C1 DOMAIN OF MUNC13-1.
JRNL REF BIOCHEMISTRY V. 44 1089 2005
JRNL REFN ISSN 0006-2960
JRNL PMID 15667202
JRNL DOI 10.1021/BI0476127
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1C, CNS 0.9
REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 861 RESTRAINTS WERE USED FOR
REMARK 3 THE FINAL CALCULATIONS, INCLUDING 781 NOES (OF WHICH 384 WERE
REMARK 3 LONG-RANGE NOES), 30 HYDROGEN BOND RESTRAINTS, 50 TORSION ANGLE
REMARK 3 RESTRAINTS AND 18 RESTRAINTS FOR THE TWO ZN2+ BINDING SITES. THE
REMARK 3 LATTER WERE DERIVED FROM ANALYSIS OF HIGH RESOLUTION CRYSTAL
REMARK 3 STRUCTURES CONTAINING BOUND ZN2+ IONS THAT ARE COORDINATED BY
REMARK 3 THREE CYSTEINES AND ONE HISTIDINE
REMARK 4
REMARK 4 1Y8F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-04.
REMARK 100 THE DEPOSITION ID IS D_1000031246.
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 : 150MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.5MM MUNC13-1 C1-DOMAIN U-15N,
REMARK 210 40MM HEPES (PH 7.0), 150MM NACL,
REMARK 210 50UM ZNCL2; 1.5MM MUNC13-1 C1-
REMARK 210 DOMAIN U-15N,13C, 40MM HEPES (PH
REMARK 210 7.0), 150MM NACL, 50UM ZNCL2
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; 3D_13C-
REMARK 210 SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 2.3, NMRVIEW 4.1.2,
REMARK 210 TALOS 2003.027.13.05
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 2000
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH LOWEST NOE
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD TRIPLE
REMARK 210 RESONANCE TECHNIQUES
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 GLY A 554
REMARK 465 SER A 555
REMARK 465 PRO A 556
REMARK 465 GLY A 557
REMARK 465 ILE A 558
REMARK 465 SER A 559
REMARK 465 GLY A 560
REMARK 465 GLY A 561
REMARK 465 GLY A 562
REMARK 465 GLY A 563
REMARK 465 GLY A 564
REMARK 465 ILE A 565
REMARK 465 LYS A 617
REMARK 465 LEU A 618
REMARK 465 ASN A 619
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 O MET A 595 H CYS A 604 1.59
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 LEU A 587 40.74 -95.04
REMARK 500 1 TRP A 588 -165.06 -108.44
REMARK 500 1 ILE A 590 -61.49 -131.42
REMARK 500 1 GLN A 593 158.68 -42.46
REMARK 500 1 THR A 598 30.75 -98.38
REMARK 500 1 GLU A 599 -39.44 -139.51
REMARK 500 1 ASP A 615 39.65 -176.48
REMARK 500 2 LEU A 587 39.51 -94.01
REMARK 500 2 TRP A 588 -168.58 -108.36
REMARK 500 2 ILE A 590 -62.07 -127.23
REMARK 500 2 GLN A 593 152.40 -42.75
REMARK 500 2 THR A 598 31.30 -99.18
REMARK 500 2 GLU A 599 -40.77 -140.37
REMARK 500 2 ASP A 615 41.76 -161.06
REMARK 500 3 LEU A 587 41.94 -93.73
REMARK 500 3 TRP A 588 -165.91 -111.01
REMARK 500 3 ILE A 590 -61.18 -132.58
REMARK 500 3 GLN A 593 156.15 -41.41
REMARK 500 3 GLU A 599 -41.30 -136.42
REMARK 500 3 ASP A 615 39.67 -161.10
REMARK 500 4 LEU A 587 41.09 -94.38
REMARK 500 4 TRP A 588 -166.74 -108.82
REMARK 500 4 ILE A 590 -61.75 -125.07
REMARK 500 4 GLN A 593 157.20 -43.56
REMARK 500 4 THR A 598 31.31 -99.02
REMARK 500 4 GLU A 599 -40.39 -140.05
REMARK 500 4 ASN A 613 -168.04 -61.25
REMARK 500 4 ASP A 615 39.47 -167.39
REMARK 500 5 LEU A 587 38.88 -94.55
REMARK 500 5 ILE A 590 -69.02 68.86
REMARK 500 5 THR A 598 31.41 -98.92
REMARK 500 5 GLU A 599 -41.36 -139.95
REMARK 500 5 ASP A 615 59.62 -170.49
REMARK 500 6 LEU A 587 39.75 -94.62
REMARK 500 6 TRP A 588 -165.69 -109.20
REMARK 500 6 ILE A 590 -61.98 -126.00
REMARK 500 6 GLN A 593 156.66 -43.04
REMARK 500 6 THR A 598 30.35 -98.65
REMARK 500 6 GLU A 599 -40.79 -141.29
REMARK 500 6 ASN A 613 -177.82 -60.72
REMARK 500 6 ASP A 615 39.57 -157.39
REMARK 500 7 ALA A 574 109.43 -59.30
REMARK 500 7 LEU A 587 39.22 -94.03
REMARK 500 7 ILE A 590 -65.76 69.34
REMARK 500 7 GLN A 593 156.43 -37.83
REMARK 500 7 THR A 598 31.03 -99.01
REMARK 500 7 GLU A 599 -40.01 -140.12
REMARK 500 7 ASP A 615 39.84 -171.26
REMARK 500 8 LEU A 587 38.93 -94.02
REMARK 500 8 ILE A 590 -60.46 -139.98
REMARK 500
REMARK 500 THIS ENTRY HAS 133 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 701 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 567 ND1
REMARK 620 2 CYS A 597 SG 105.1
REMARK 620 3 CYS A 600 SG 100.9 120.0
REMARK 620 4 CYS A 616 SG 114.4 111.8 104.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 702 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 580 SG
REMARK 620 2 CYS A 583 SG 110.5
REMARK 620 3 HIS A 605 ND1 100.4 115.2
REMARK 620 4 CYS A 608 SG 103.9 99.9 126.1
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 702
DBREF 1Y8F A 567 616 UNP Q62768 UN13A_RAT 567 616
SEQADV 1Y8F GLY A 554 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F SER A 555 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F PRO A 556 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F GLY A 557 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F ILE A 558 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F SER A 559 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F GLY A 560 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F GLY A 561 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F GLY A 562 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F GLY A 563 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F GLY A 564 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F ILE A 565 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F GLN A 566 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F LYS A 617 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F LEU A 618 UNP Q62768 CLONING ARTIFACT
SEQADV 1Y8F ASN A 619 UNP Q62768 CLONING ARTIFACT
SEQRES 1 A 66 GLY SER PRO GLY ILE SER GLY GLY GLY GLY GLY ILE GLN
SEQRES 2 A 66 HIS ASN PHE GLU VAL TRP THR ALA THR THR PRO THR TYR
SEQRES 3 A 66 CYS TYR GLU CYS GLU GLY LEU LEU TRP GLY ILE ALA ARG
SEQRES 4 A 66 GLN GLY MET ARG CYS THR GLU CYS GLY VAL LYS CYS HIS
SEQRES 5 A 66 GLU LYS CYS GLN ASP LEU LEU ASN ALA ASP CYS LYS LEU
SEQRES 6 A 66 ASN
HET ZN A 701 1
HET ZN A 702 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 LYS A 607 LEU A 612 1 6
SHEET 1 A 3 PHE A 569 THR A 573 0
SHEET 2 A 3 GLN A 593 CYS A 597 -1 O ARG A 596 N GLU A 570
SHEET 3 A 3 LYS A 603 CYS A 604 -1 O CYS A 604 N MET A 595
LINK ND1 HIS A 567 ZN ZN A 701 1555 1555 2.30
LINK SG CYS A 580 ZN ZN A 702 1555 1555 2.37
LINK SG CYS A 583 ZN ZN A 702 1555 1555 2.51
LINK SG CYS A 597 ZN ZN A 701 1555 1555 2.50
LINK SG CYS A 600 ZN ZN A 701 1555 1555 2.36
LINK ND1 HIS A 605 ZN ZN A 702 1555 1555 2.29
LINK SG CYS A 608 ZN ZN A 702 1555 1555 2.31
LINK SG CYS A 616 ZN ZN A 701 1555 1555 2.50
SITE 1 AC1 5 HIS A 567 CYS A 597 GLU A 599 CYS A 600
SITE 2 AC1 5 CYS A 616
SITE 1 AC2 4 CYS A 580 CYS A 583 HIS A 605 CYS A 608
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
Complete list - r 2 2 Bytes