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- PDB-3g5c: Structural and biochemical studies on the ectodomain of human ADAM22 -

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Basic information

Entry
Database: PDB / ID: 3g5c
TitleStructural and biochemical studies on the ectodomain of human ADAM22
ComponentsADAM 22
KeywordsMEMBRANE PROTEIN / alpha/beta fold / cross-linked domain / Cell adhesion / Cleavage on pair of basic residues / EGF-like domain / Glycoprotein / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


LGI-ADAM interactions / negative regulation of cell adhesion / central nervous system development / metalloendopeptidase activity / integrin binding / cell adhesion / axon / proteolysis / membrane / plasma membrane
Similarity search - Function
ADAM cysteine-rich / Disintegrin domain / Echistatin / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type ...ADAM cysteine-rich / Disintegrin domain / Echistatin / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / EGF-like domain, extracellular / EGF-like domain / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / EGF-like domain signature 1. / EGF-like domain / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combined with SIRAS / Resolution: 2.36 Å
AuthorsLiu, H. / Shim, A. / Chen, X. / He, X.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and biochemical studies on the ectodomain of human ADAM22
Authors: Liu, H. / Shim, A. / Chen, X. / He, X.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAM 22
B: ADAM 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,05914
Polymers112,4912
Non-polymers1,56812
Water6,648369
1
A: ADAM 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0307
Polymers56,2461
Non-polymers7846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADAM 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0307
Polymers56,2461
Non-polymers7846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.090, 122.090, 208.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ADAM 22 / A disintegrin and metalloproteinase domain 22 / Metalloproteinase-like / disintegrin-like / and ...A disintegrin and metalloproteinase domain 22 / Metalloproteinase-like / disintegrin-like / and cysteine-rich protein 2 / Metalloproteinase-disintegrin ADAM22-3


Mass: 56245.715 Da / Num. of mol.: 2 / Fragment: M, D, C and E domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM22, MDC2 / Plasmid: PAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9P0K1
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2008 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→94.49 Å / Num. all: 51529 / Num. obs: 49760 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.44 / Num. unique all: 5641 / Rsym value: 0.389 / % possible all: 91.5

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
SOLVEphasing
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: combined with SIRAS
Starting model: PDB ENTRY 1R54 AND 2ERO

1r54

2ero


Resolution: 2.36→50 Å / Isotropic thermal model: anisotropic / Cross valid method: througout / σ(F): 0 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 4660 -RANDOM
Rwork0.2446 ---
all-47704 --
obs-46287 97 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.168 Å21.073 Å20 Å2
2--9.168 Å20 Å2
3----18.336 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.67 Å
Refinement stepCycle: LAST / Resolution: 2.36→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7456 0 90 369 7915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 2.36→2.51 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.434 759 -
Rwork0.42 --
obs-6592 92.9 %

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