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- PDB-3ph9: Crystal structure of the human anterior gradient protein 3 -

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Basic information

Entry
Database: PDB / ID: 3ph9
TitleCrystal structure of the human anterior gradient protein 3
ComponentsAnterior gradient protein 3 homolog
KeywordsISOMERASE / Thioredoxin fold / protein disulfide isomerase / endoplasmic reticulum
Function / homology
Function and homology information


: / dystroglycan binding / intracellular membrane-bounded organelle / endoplasmic reticulum
Similarity search - Function
Thioredoxin-like / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Anterior gradient protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsNguyen, V.D. / Ruddock, L.W. / Salin, M. / Wierenga, R.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2018
Title: Crystal structure of human anterior gradient protein 3.
Authors: Nguyen, V.D. / Biterova, E. / Salin, M. / Wierenga, R.K. / Ruddock, L.W.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Sep 6, 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: Anterior gradient protein 3 homolog
B: Anterior gradient protein 3 homolog


Theoretical massNumber of molelcules
Total (without water)35,8652
Polymers35,8652
Non-polymers00
Water5,224290
1
A: Anterior gradient protein 3 homolog


Theoretical massNumber of molelcules
Total (without water)17,9331
Polymers17,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anterior gradient protein 3 homolog


Theoretical massNumber of molelcules
Total (without water)17,9331
Polymers17,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.290, 71.450, 59.810
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A10 - 127
2116B10 - 127

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Components

#1: Protein Anterior gradient protein 3 homolog / AG-3 / AG3 / hAG-3 / Breast cancer membrane protein 11


Mass: 17932.678 Da / Num. of mol.: 2 / Fragment: Anterior gradient protein 3
Source method: isolated from a genetically manipulated source
Details: Cytoplasmic / Source: (gene. exp.) Homo sapiens (human) / Gene: AGR3, BCMP11, UNQ642/PRO1272 / Plasmid: pet23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: Q8TD06, protein disulfide-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 1.97 Å3/Da / Density % sol: 37.41 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25 % PEG 4000, 0.2 M MgCl2, 0.2 M NaCl, 0.1 M Tris-Cl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 11, 2006
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 24330 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SEN

1sen


Resolution: 1.83→45.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.642 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 1228 5 %RANDOM
Rwork0.17697 ---
obs0.17968 23102 99.06 %-
all-24330 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.492 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.43 Å2
2--0.23 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.83→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 0 290 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222255
X-RAY DIFFRACTIONr_bond_other_d0.0010.021568
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9643046
X-RAY DIFFRACTIONr_angle_other_deg0.91533825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02224.69113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8781514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.51342
X-RAY DIFFRACTIONr_mcbond_other0.1941.5536
X-RAY DIFFRACTIONr_mcangle_it1.33322176
X-RAY DIFFRACTIONr_scbond_it2.1783913
X-RAY DIFFRACTIONr_scangle_it3.534.5870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1671 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.445
loose thermal1.2610
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 82 -
Rwork0.2 1706 -
obs--98.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73360.0084-0.13110.4646-0.01390.76320.03370.07440.0148-0.0214-0.0243-0.0518-0.0239-0.0468-0.00930.00370.0070.0050.01420.00850.010213.95738.0741.82
20.881-0.0949-0.04530.43260.10730.75830.0112-0.0622-0.01190.01720.02460.0271-0.0030.0352-0.03580.00110.00010.00220.00790.0040.011913.26943.7963.481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 127
2X-RAY DIFFRACTION2B31 - 127

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