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- PDB-1szh: Crystal Structure of C. elegans HER-1 -

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Basic information

Entry
Database: PDB / ID: 1szh
TitleCrystal Structure of C. elegans HER-1
ComponentsHer-1 protein
KeywordsSIGNALING PROTEIN / extended 3-10 helix / left-handed anti-parallel 4-helix bundle / overhand 3-helix bundle
Function / homology
Function and homology information


male sex determination / signaling receptor binding / extracellular region
Similarity search - Function
DNA polymerase; domain 1 - #360 / Caenorhabditis elegans Her-1, C-terminal domain / Protein Her-1 / Her-1 superfamily / Her-1, C-terminal / Caenorhabditis elegans Her-1 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Protein her-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsHamaoka, B.Y. / Dann III, C.E. / Geisbrecht, B.V. / Leahy, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of Caenorhabditis elegans HER-1 and characterization of the interaction between HER-1 and TRA-2A.
Authors: Hamaoka, B.Y. / Dann III, C.E. / Geisbrecht, B.V. / Leahy, D.J.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Her-1 protein
B: Her-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0896
Polymers36,8532
Non-polymers2364
Water4,378243
1
A: Her-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5443
Polymers18,4261
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Her-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5443
Polymers18,4261
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.970, 58.930, 99.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Her-1 protein


Mass: 18426.342 Da / Num. of mol.: 2 / Mutation: N98E, N163E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: HER-1, ZK287.8 / Plasmid: pSGHV0 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P34704
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: PEG 3350, sodium acetate, ammonijm sulfate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97931, 0.97917, 0.96866
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979171
30.968661
ReflectionResolution: 1.5→29.46 Å / Num. all: 50321 / Num. obs: 50045 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.8 Å2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 80.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.46 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 720128.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2378 5 %RANDOM
Rwork0.209 ---
all0.21 50321 --
obs0.209 47341 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1296 Å2 / ksol: 0.393968 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--8.87 Å20 Å2
3----8.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 16 243 2564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it2.721.5
X-RAY DIFFRACTIONc_mcangle_it3.682
X-RAY DIFFRACTIONc_scbond_it5.362
X-RAY DIFFRACTIONc_scangle_it7.752.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.365 215 5.4 %
Rwork0.335 3784 -
obs-3992 80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMACETATE_TOPOLOGY.FIL
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5ACETATE_PARAMETER.FIL

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