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- PDB-1h4u: Domain G2 of mouse nidogen-1 -

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Basic information

Entry
Database: PDB / ID: 1h4u
TitleDomain G2 of mouse nidogen-1
ComponentsNIDOGEN-1
KeywordsEXTRACELLULAR MATRIX PROTEIN
Function / homology
Function and homology information


Laminin interactions / regulation of basement membrane organization / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / Degradation of the extracellular matrix / protein complex involved in cell-matrix adhesion / extracellular matrix binding / proteoglycan binding / positive regulation of cell-substrate adhesion ...Laminin interactions / regulation of basement membrane organization / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / Degradation of the extracellular matrix / protein complex involved in cell-matrix adhesion / extracellular matrix binding / proteoglycan binding / positive regulation of cell-substrate adhesion / positive regulation of muscle cell differentiation / basement membrane / collagen binding / extracellular matrix organization / extracellular matrix / positive regulation of cell adhesion / cell-matrix adhesion / cell periphery / : / calcium ion binding / extracellular region
Similarity search - Function
NIDO domain / G2 nidogen/fibulin G2F / Nidogen-like / G2F domain / Nidogen G2 beta-barrel domain profile. / NIDO domain profile. / Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins. / G2 nidogen domain and fibulin / EGF domain / EGF domain ...NIDO domain / G2 nidogen/fibulin G2F / Nidogen-like / G2F domain / Nidogen G2 beta-barrel domain profile. / NIDO domain profile. / Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins. / G2 nidogen domain and fibulin / EGF domain / EGF domain / : / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Green Fluorescent Protein / Green fluorescent protein / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Green fluorescent protein / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsHopf, M. / Gohring, W. / Ries, A. / Timpl, R. / Hohenester, E.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal Structure and Mutational Analysis of a Perlecan-Binding Fragment of Nidogen-1
Authors: Hopf, M. / Gohring, W. / Ries, A. / Timpl, R. / Hohenester, E.
#1: Journal: Embo J. / Year: 1991
Title: Recombinant Nidogen Consists of Three Globular Domains and Mediates Binding of Laminin to Collagen Type Iv
Authors: Fox, J.W. / Mayer, U. / Nischt, R. / Aumailley, M. / Reinhardt, D. / Wiedemann, H. / Mann, K. / Timpl, R. / Krieg, T. / Engel, J. / Chu, M.-L.
History
DepositionMay 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NIDOGEN-1


Theoretical massNumber of molelcules
Total (without water)29,2731
Polymers29,2731
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.180, 95.180, 65.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein NIDOGEN-1


Mass: 29272.756 Da / Num. of mol.: 1 / Fragment: G2 FRAGMENT, RESIDUES 395-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P10493
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growpH: 5.5
Details: 10 MG/ML PROTEIN, 5-8% PEG4000, 0.1 M ACETATE PH 5.5
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.01 Mammonium carbonate1drop
35-8 %(w/v)PEG40001reservoir
40.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: QUANTUM4 / Detector: CCD / Date: Aug 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 17203 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.8 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 15 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→15 Å / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1713 10 %RANDOM
Rwork0.241 ---
obs0.241 17188 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 75 1984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.32
X-RAY DIFFRACTIONc_scbond_it3.22
X-RAY DIFFRACTIONc_scangle_it4.62.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS

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