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- PDB-1i1j: STRUCTURE OF MELANOMA INHIBITORY ACTIVITY PROTEIN: A MEMBER OF A ... -

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Basic information

Entry
Database: PDB / ID: 1i1j
TitleSTRUCTURE OF MELANOMA INHIBITORY ACTIVITY PROTEIN: A MEMBER OF A NEW FAMILY OF SECRETED PROTEINS
ComponentsMELANOMA DERIVED GROWTH REGULATORY PROTEIN
KeywordsHORMONE/GROWTH FACTOR / SH3 subdomain / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


extracellular matrix organization / growth factor activity / extracellular space
Similarity search - Function
Melanoma-derived growth regulatory protein / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Melanoma-derived growth regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.39 Å
AuthorsLougheed, J.C. / Holton, J.M. / Alber, T. / Bazan, J.F. / Handel, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins.
Authors: Lougheed, J.C. / Holton, J.M. / Alber, T. / Bazan, J.F. / Handel, T.M.
History
DepositionFeb 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MELANOMA DERIVED GROWTH REGULATORY PROTEIN
B: MELANOMA DERIVED GROWTH REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,5162
Polymers24,5162
Non-polymers00
Water3,819212
1
A: MELANOMA DERIVED GROWTH REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,2581
Polymers12,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MELANOMA DERIVED GROWTH REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,2581
Polymers12,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.534, 48.396, 87.774
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 MELANOMA DERIVED GROWTH REGULATORY PROTEIN / MELANOMA INHIBITORY ACTIVITY


Mass: 12258.138 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q16674
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG 8000, Tris, sodium chloride, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 4.55
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.5 mg/mlprotein1drop
210 mMacetate1drop
30.02 %azide1drop
4100 mMTris1reservoir
58 %PEG80001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9791, 0.9794, 1.0332
SYNCHROTRONSSRL BL9-221
SYNCHROTRONALS 5.0.231
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 26, 2000
ADSC QUANTUM 42CCDFeb 26, 2000
ADSC QUANTUM 43CCDJan 25, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 FlatMADMx-ray1
2Si 111 FlatSINGLE WAVELENGTHMx-ray1
3Si 111 FlatSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
31.03321
411
ReflectionResolution: 1.39→43.85 Å / Num. all: 47146 / Num. obs: 47146 / % possible obs: 97.76 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 18.141 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 16.8
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Num. unique all: 15627 / Rsym value: 0.24 / % possible all: 91.5
Reflection
*PLUS
% possible obs: 99.44 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
MLPHAREphasing
REFMACrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.39→43.85 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber 1991
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2019 -RANDOM
Rwork0.208 ---
all0.2087 47146 --
obs0.2087 47146 100 %-
Refinement stepCycle: LAST / Resolution: 1.39→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 0 212 1866
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.031
X-RAY DIFFRACTIONp_bond_d0.014
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): -3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.35 Å2

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