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- PDB-1jiq: Crystal Structure of Human Autocrine Motility Factor -

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Basic information

Entry
Database: PDB / ID: 1jiq
TitleCrystal Structure of Human Autocrine Motility Factor
Componentsautocrine motility factor
KeywordsISOMERASE / cytokine / Autocrine Motility Factor
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / humoral immune response / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / cytokine activity / gluconeogenesis / response to progesterone / glycolytic process / TP53 Regulates Metabolic Genes / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / ficolin-1-rich granule lumen / carbohydrate metabolic process / learning or memory / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTanaka, N. / Haga, A. / Uemura, H. / Akiyama, H. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Inhibition mechanism of cytokine activity of human autocrine motility factor examined by crystal structure analyses and site-directed mutagenesis studies.
Authors: Tanaka, N. / Haga, A. / Uemura, H. / Akiyama, H. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T.
History
DepositionJul 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: autocrine motility factor
B: autocrine motility factor
C: autocrine motility factor
D: autocrine motility factor


Theoretical massNumber of molelcules
Total (without water)252,9204
Polymers252,9204
Non-polymers00
Water26,5721475
1
A: autocrine motility factor
B: autocrine motility factor


Theoretical massNumber of molelcules
Total (without water)126,4602
Polymers126,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-74 kcal/mol
Surface area37000 Å2
MethodPISA
2
C: autocrine motility factor
D: autocrine motility factor


Theoretical massNumber of molelcules
Total (without water)126,4602
Polymers126,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12960 Å2
ΔGint-71 kcal/mol
Surface area36890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.77, 107.4, 270.7
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer. Two dimers exist in an asymmetric unit.

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Components

#1: Protein
autocrine motility factor / glucose phosphate isomerase


Mass: 63229.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1475 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, sodium acetate, PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2000
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 183404 / % possible obs: 98.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 4.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / % possible all: 92.1

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DQR

1dqr


Resolution: 1.9→36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.203 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19791 9195 5 %RANDOM
Rwork0.16747 ---
obs0.169 174100 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.102 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17780 0 0 1475 19255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02118216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216316
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.93124660
X-RAY DIFFRACTIONr_angle_other_deg0.759338000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.13132224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32153297
X-RAY DIFFRACTIONr_chiral_restr0.0860.22680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220268
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023760
X-RAY DIFFRACTIONr_nbd_refined0.2280.34209
X-RAY DIFFRACTIONr_nbd_other0.1960.316429
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.51395
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1510.510
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.533
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.591.511064
X-RAY DIFFRACTIONr_mcangle_it1.089217832
X-RAY DIFFRACTIONr_scbond_it1.74737152
X-RAY DIFFRACTIONr_scangle_it2.8664.56828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 593
Rwork0.206 11476

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