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- PDB-1vkk: Crystal structure of Glia maturation factor-gamma (GMFG) from Mus... -

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Basic information

Entry
Database: PDB / ID: 1vkk
TitleCrystal structure of Glia maturation factor-gamma (GMFG) from Mus musculus at 1.50 A resolution
ComponentsGlia maturation factor gamma
KeywordsHORMONE/GROWTH FACTOR / 15079298 / GMFG / GLIA MATURATION FACTOR-GAMMA / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


actin filament debranching / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / Neutrophil degranulation / growth factor activity / actin binding
Similarity search - Function
Glia maturation factor / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Glia maturation factor gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Glia maturation factor-gamma (GMFG) from Mus musculus at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glia maturation factor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3282
Polymers18,2331
Non-polymers951
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.049, 34.605, 38.365
Angle α, β, γ (deg.)69.95, 87.51, 70.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glia maturation factor gamma / GMF-gamma


Mass: 18232.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GMFG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ERL7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.81 Å3/Da / Density % sol: 31.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 30% PEG-4000, 0.1M Tris hydrochloride pH 8.5,0.2M lithium sulfate monohydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Oct 8, 2003
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→35.92 Å / Num. obs: 22189 / % possible obs: 76.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 22.11 Å2 / Rsym value: 0.044 / Net I/σ(I): 16.4
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 518 / Rsym value: 0.38 / % possible all: 23.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f7s

1f7s


Resolution: 1.35→35.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.954 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ARG 142 SIDE CHAIN CONFORMATION IS SUSPICIOUS. ITS DENSITY IS POOR. 3. THE NOMINAL RESOLUTION IS 1.50 A WITH 2779 OBSERVED REFLECTIONS ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ARG 142 SIDE CHAIN CONFORMATION IS SUSPICIOUS. ITS DENSITY IS POOR. 3. THE NOMINAL RESOLUTION IS 1.50 A WITH 2779 OBSERVED REFLECTIONS BETWEEN 1.50-1.35A (35% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. 4. TEMPERATURE FACTORS WERE REFINED AS ISOTROPIC
RfactorNum. reflection% reflectionSelection details
Rfree0.19411 1141 5.1 %RANDOM
Rwork0.1581 ---
obs0.15996 21048 76.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.34 Å2-0.31 Å2
2---0.24 Å2-0.02 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.35→35.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 5 183 1321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221183
X-RAY DIFFRACTIONr_bond_other_d0.0010.021087
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9721599
X-RAY DIFFRACTIONr_angle_other_deg0.83632546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28323.96658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45615230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9451510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined0.230.2254
X-RAY DIFFRACTIONr_nbd_other0.1920.21156
X-RAY DIFFRACTIONr_nbtor_other0.0910.2787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.226
X-RAY DIFFRACTIONr_mcbond_it1.9953722
X-RAY DIFFRACTIONr_mcbond_other0.4993274
X-RAY DIFFRACTIONr_mcangle_it2.81251154
X-RAY DIFFRACTIONr_scbond_it4.188514
X-RAY DIFFRACTIONr_scangle_it6.30211444
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 25 4.83 %
Rwork0.27 493 -
Refinement TLS params.Method: refined / Origin x: -0.052 Å / Origin y: 1.213 Å / Origin z: -1.971 Å
111213212223313233
T-0.036 Å2-0.0082 Å2-0.0098 Å2--0.0306 Å2-0.0047 Å2---0.033 Å2
L0.558 °2-0.1563 °2-0.1032 °2-1.1806 °2-0.1889 °2--1.5612 °2
S0.0059 Å °0.0019 Å °0.0092 Å °-0.0262 Å °0.0193 Å °0.033 Å °0.0016 Å °-0.005 Å °-0.0252 Å °
Refinement TLS groupSelection: ALL

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