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- PDB-7aah: Structure of human pERp1 -

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Basic information

Entry
Database: PDB / ID: 7aah
TitleStructure of human pERp1
ComponentsMarginal zone B- and B1-cell-specific protein
KeywordsIMMUNE SYSTEM / Folding factor / Endoplasmatic Reticulum / IgM
Function / homology
Function and homology information


regulation of B cell proliferation / regulation of insulin receptor signaling pathway / endoplasmic reticulum chaperone complex / integrin activation / positive regulation of immunoglobulin production / regulation of cell population proliferation / endoplasmic reticulum lumen / apoptotic process / positive regulation of cell population proliferation / extracellular region / cytoplasm
Similarity search - Function
Domain of unknown function DUF3456 / TLR4 regulator and MIR-interacting MSAP / Endoplasmic reticulum targeting sequence.
Similarity search - Domain/homology
CITRIC ACID / Marginal zone B- and B1-cell-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.4 Å
AuthorsSowa, S.T. / Moilanen, A. / Biterova, E. / Saaranen, M.J. / Lehtio, L. / Ruddock, L.W.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland266457 Finland
CitationJournal: J.Mol.Biol. / Year: 2021
Title: High-resolution Crystal Structure of Human pERp1, A Saposin-like Protein Involved in IgA, IgM and Integrin Maturation in the Endoplasmic Reticulum.
Authors: Sowa, S.T. / Moilanen, A. / Biterova, E. / Saaranen, M.J. / Lehtio, L. / Ruddock, L.W.
History
DepositionSep 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Marginal zone B- and B1-cell-specific protein
B: Marginal zone B- and B1-cell-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7073
Polymers36,5152
Non-polymers1921
Water5,621312
1
A: Marginal zone B- and B1-cell-specific protein


Theoretical massNumber of molelcules
Total (without water)18,2571
Polymers18,2571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Marginal zone B- and B1-cell-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4502
Polymers18,2571
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.714, 63.909, 71.889
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 Marginal zone B- and B1-cell-specific protein / Mesenteric estrogen-dependent adipose 7 / MEDA-7 / Plasma cell-induced resident endoplasmic ...Mesenteric estrogen-dependent adipose 7 / MEDA-7 / Plasma cell-induced resident endoplasmic reticulum protein / pERp1 / Proapoptotic caspase adapter protein


Mass: 18257.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MZB1, MEDA7, PACAP, HSPC190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WU39
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Lithium citrate tribasic tetrahydrate, Glycerol ethoxylate, n-decyl-beta-D-maltopyranoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.4→47.8 Å / Num. obs: 58099 / % possible obs: 99.1 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 12.88
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 5426 / CC1/2: 0.364

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.4→47.764 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1857 2896 5 %
Rwork0.1467 --
obs0.1487 57970 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→47.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 13 312 2515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082435
X-RAY DIFFRACTIONf_angle_d0.9643328
X-RAY DIFFRACTIONf_dihedral_angle_d22.172945
X-RAY DIFFRACTIONf_chiral_restr0.077347
X-RAY DIFFRACTIONf_plane_restr0.007449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42270.39391160.38372299X-RAY DIFFRACTION88
1.4227-1.44730.36171320.3092473X-RAY DIFFRACTION95
1.4473-1.47360.2971360.27082586X-RAY DIFFRACTION99
1.4736-1.50190.2891390.24662629X-RAY DIFFRACTION100
1.5019-1.53260.29331350.24262592X-RAY DIFFRACTION100
1.5326-1.56590.23441380.23012623X-RAY DIFFRACTION100
1.5659-1.60240.23661390.19452627X-RAY DIFFRACTION100
1.6024-1.64240.21851370.17432612X-RAY DIFFRACTION100
1.6424-1.68680.19561380.15622612X-RAY DIFFRACTION100
1.6868-1.73650.20091380.14142610X-RAY DIFFRACTION100
1.7365-1.79250.18711380.13842625X-RAY DIFFRACTION100
1.7925-1.85660.1881390.1362648X-RAY DIFFRACTION100
1.8566-1.93090.20181390.14562638X-RAY DIFFRACTION100
1.9309-2.01880.17511380.13522629X-RAY DIFFRACTION100
2.0188-2.12530.16811410.13162665X-RAY DIFFRACTION100
2.1253-2.25840.18741380.12722635X-RAY DIFFRACTION100
2.2584-2.43280.15951390.12642646X-RAY DIFFRACTION100
2.4328-2.67760.16851420.12822687X-RAY DIFFRACTION100
2.6776-3.0650.17651410.13532671X-RAY DIFFRACTION100
3.065-3.86130.15491430.12962724X-RAY DIFFRACTION100

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