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- PDB-1sen: Endoplasmic reticulum protein Rp19 O95881 -

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Basic information

Entry
Database: PDB / ID: 1sen
TitleEndoplasmic reticulum protein Rp19 O95881
ComponentsThioredoxin-like protein p19
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Endoplasmic reticulum / Rp19 / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


protein-disulfide reductase (glutathione) / protein-disulfide reductase (glutathione) activity / protein-disulfide reductase activity / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
ERp19 / Thioredoxin-like / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Thioredoxin domain-containing protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.199 Å
AuthorsLiu, Z.-J. / Chen, L. / Tempel, W. / Shah, A. / Lee, D. / Dailey, T.A. / Mayer, M.R. / Rose, J.P. / Richardson, D.C. / Richardson, J.S. ...Liu, Z.-J. / Chen, L. / Tempel, W. / Shah, A. / Lee, D. / Dailey, T.A. / Mayer, M.R. / Rose, J.P. / Richardson, D.C. / Richardson, J.S. / Dailey, H.A. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1997
Title: Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Authors: Murshudov, G.N. / Vagin, A.A. / Dodson, E.J.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999
Title: Automated MAD and MIR structure solution
Authors: Terwilliger, T.C. / Berendzen, J.
#3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2000
Title: Maximum likelihood density modification
Authors: Terwilliger, T.C.
#4: Journal: Nat.Struct.Biol. / Year: 1999
Title: Automated protein model building combined with iterative structure refinement
Authors: Perrakis, A. / Morris, R. / Lamzin, V.S.
History
DepositionFeb 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-like protein p19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8016
Polymers18,3041
Non-polymers4975
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.986, 50.556, 59.386
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 Thioredoxin-like protein p19 / Endoplasmic reticulum protein ERp19


Mass: 18304.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The protein was cloned, expressed and purified by the SECSG human protein production group (T.A. Dailey, M. Mayer) under the direction of H.A. Dailey.
Gene: TLP19 / Production host: Escherichia coli (E. coli) / References: UniProt: O95881
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 291 K / Method: modified batch crystallization / pH: 7
Details: 12% PEG 4000, 100mM Na Hepes, 100mM NaCl, pH 7.0, modified batch crystallization, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.07 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.199→38.633 Å / Num. all: 42206 / Num. obs: 42206 / Observed criterion σ(I): -3

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Phasing

PhasingMethod: MIR
Phasing dmFOM : 0.53 / FOM acentric: 0.51 / FOM centric: 0.6 / Reflection: 7438 / Reflection acentric: 6336 / Reflection centric: 1102
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-19.1680.770.770.74418264154
3.8-60.80.80.781209948261
3-3.80.720.720.7114821240242
2.6-30.560.570.5314511257194
2.3-2.60.290.290.2822111996215
2.1-2.30.170.160.2266763136
Phasing MIRResolution: 2.5→20 Å / FOM: 0.33 / Reflection: 5250
Phasing MIR shell
Resolution (Å)FOMReflection
8.52-200.32303
5.54-8.520.38450
4.38-5.540.35568
3.74-4.380.34653
3.31-3.740.33734
3-3.310.34789
2.77-30.35847
2.58-2.770.27906

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.1.24refinement
SOLVE2.03phasing
RESOLVE2.03phasing
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.199→38.633 Å / Cor.coef. Fo:Fc: 0.965 / SU R Cruickshank DPI: 0.041 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 2115 5.011 %random
Rwork0.1616 ---
all0.163 42206 --
obs-42206 --
Solvent computationSolvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 12.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.069 Å20 Å20 Å2
2--0.077 Å20 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.199→38.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 6 97 1170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0110.0211102
X-RAY DIFFRACTIONp_angle_d5.5385138
X-RAY DIFFRACTIONp_mcbond_it1.9762682
X-RAY DIFFRACTIONp_scbond_it2.5562420
X-RAY DIFFRACTIONp_mcangle_it2.77731104
X-RAY DIFFRACTIONp_scangle_it3.473390
X-RAY DIFFRACTIONp_chiral_restr0.0960.2156
X-RAY DIFFRACTIONp_planar_restr0.0080.02848
X-RAY DIFFRACTIONp_xyhbond_nbd0.0610.274
X-RAY DIFFRACTIONp_xhyhbond_nbd0.0680.25
X-RAY DIFFRACTIONp_singtor_nbd5.5385138
X-RAY DIFFRACTIONp_multtor_nbd0.3080.2773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.199-1.23030.275870.23314053404
1.23-1.26390.215930.20219813366
1.264-1.30050.21440.17424533223
1.301-1.34050.1911430.14428433152
1.341-1.38440.1551280.12628093046
1.384-1.43290.1561560.12227292979
1.433-1.4870.1291270.11626582871
1.487-1.54760.1331440.10925342733
1.548-1.61630.1441390.11324652665
1.616-1.6950.1291210.11923802551
1.695-1.78650.153910.13922972415
1.787-1.89460.1971250.15121412300
1.895-2.02510.1491010.1620332158
2.025-2.18690.1961080.16519042021
2.187-2.39480.172860.16917681865
2.395-2.67620.2281010.19615971706
2.676-3.08770.232840.19914301516
3.088-3.77570.169620.16912261298
3.776-5.31430.184500.1639371027
5.314-38.63340.327250.26501623

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