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- PDB-1smb: Crystal Structure of Golgi-Associated PR-1 protein -

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Basic information

Entry
Database: PDB / ID: 1smb
TitleCrystal Structure of Golgi-Associated PR-1 protein
Components17kD fetal brain protein
KeywordsUNKNOWN FUNCTION / ALPHA-BETA-ALPHA
Function / homology
Function and homology information


positive regulation of epithelial cell migration / positive regulation of epithelial to mesenchymal transition / positive regulation of ERK1 and ERK2 cascade / Golgi membrane / protein homodimerization activity / extracellular space / extracellular exosome
Similarity search - Function
Golgi-associated plant pathogenesis-related protein 1, SCP domain / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family ...Golgi-associated plant pathogenesis-related protein 1, SCP domain / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Golgi-associated plant pathogenesis-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.55 Å
AuthorsSerrano, R.L. / Kuhn, A. / Hendricks, A. / Helms, J.B. / Sinning, I. / Groves, M.R.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structural analysis of the human Golgi-associated plant pathogenesis related protein GAPR-1 implicates dimerization as a regulatory mechanism
Authors: Serrano, R.L. / Kuhn, A. / Hendricks, A. / Helms, J.B. / Sinning, I. / Groves, M.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of a Golgi-associated PR-1-related protein (GAPR-1) that localizes to lipid-enriched microdomains
Authors: Groves, M.R. / Kuhn, A. / Hendricks, A. / Radke, S. / Serrano, R.L. / Helms, J.B. / Sinning, I.
History
DepositionMar 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 17kD fetal brain protein


Theoretical massNumber of molelcules
Total (without water)17,3401
Polymers17,3401
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.662, 73.662, 63.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsMONOMER IN ASYMMETRIC UNIT POSSIBLE DIMER IN SOLUTION (SEE CITATION)

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Components

#1: Protein 17kD fetal brain protein / GAPR-1


Mass: 17340.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAC12812 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 [DE3] / References: UniProt: Q9H4G4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (v/v) PEG 8000, 100mM Bis-Tris, 200mM magnesium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2000 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.55→28.513 Å / Num. obs: 28674 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.07 / Net I/σ(I): 6.2
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.5 / Num. unique all: 25557 / Rsym value: 0.251 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.55→28.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1169585.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 1456 5.1 %RANDOM
Rwork0.1881 ---
all-28660 --
obs-28660 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3246 Å2 / ksol: 0.410696 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.08 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 0 127 1449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 242 5.1 %
Rwork0.22 4505 -
obs-4170 98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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