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- PDB-1npu: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MURINE PD-1 -

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Basic information

Entry
Database: PDB / ID: 1npu
TitleCRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MURINE PD-1
ComponentsProgrammed cell death protein 1
KeywordsIMMUNE SYSTEM / Ig V-type domain / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / regulation of immune response / adaptive immune response / external side of plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Programmed cell death protein 1 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, X. / Schwartz, J.-C.D. / Guo, X. / Cao, E. / Chen, L. / Zhang, Z.-Y. / Nathenson, S.G. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Immunity / Year: 2004
Title: Structural and functional analysis of the costimulatory receptor programmed death-1.
Authors: Zhang, X. / Schwartz, J.C. / Guo, X. / Bhatia, S. / Cao, E. / Lorenz, M. / Cammer, M. / Chen, L. / Zhang, Z.Y. / Edidin, M.A. / Nathenson, S.G. / Almo, S.C.
History
DepositionJan 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 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: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)13,1771
Polymers13,1771
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.965, 50.802, 75.278
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 Programmed cell death protein 1 / Protein PD-1 / mPD-1


Mass: 13176.714 Da / Num. of mol.: 1 / Fragment: Ig V-type domain / Mutation: C50S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PDCD1 OR PD1 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02242
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.67 Å3/Da / Density % sol: 25.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, NaAc, NaCacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein1drop
220-30 %PEG80001reservoir
3100 mM1reservoirNaAc
4100 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9746 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9746 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 6677 / Num. obs: 6677 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 8.7 Å2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.276 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. measured all: 43650 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 97 % / Num. unique obs: 612 / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B88

1b88


Resolution: 2→18.78 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 178575.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 672 10.5 %RANDOM
Rwork0.198 ---
all0.213 6626 --
obs0.198 6425 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0753 Å2 / ksol: 0.38404 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2---3.29 Å20 Å2
3---4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 73 979
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.228 57 10.2 %
Rwork0.202 503 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.2283 / Rfactor Rwork: 0.1982
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.2275 / Rfactor Rwork: 0.2017

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