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- PDB-6gc1: Crystal structure of Trx-like and NHL repeat containing domains o... -

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Basic information

Entry
Database: PDB / ID: 6gc1
TitleCrystal structure of Trx-like and NHL repeat containing domains of human NHLRC2
ComponentsNHL repeat-containing protein 2
KeywordsUNKNOWN FUNCTION / NHL repeat containing / structural domain / protein binding / thioredoxin-like
Function / homology
Function and homology information


platelet alpha granule lumen / Platelet degranulation / extracellular region / cytosol
Similarity search - Function
NHL2, NHL repeat domain / NHL repeat profile. / Thioredoxin-like / NHL repeat / NHL repeat / Thioredoxin-like fold / Six-bladed beta-propeller, TolB-like / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...NHL2, NHL repeat domain / NHL repeat profile. / Thioredoxin-like / NHL repeat / NHL repeat / Thioredoxin-like fold / Six-bladed beta-propeller, TolB-like / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NHL repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBiterova, E. / Uusimaa, J. / Hinttala, R. / Ruddock, L.W.
Funding support Finland, 4items
OrganizationGrant numberCountry
Academy of Finland266457 Finland
Academy of Finland272573 Finland
Academy of Finland266498 Finland
Academy of Finland303996 Finland
CitationJournal: PLoS ONE / Year: 2018
Title: Structural analysis of human NHLRC2, mutations of which are associated with FINCA disease.
Authors: Biterova, E. / Ignatyev, A. / Uusimaa, J. / Hinttala, R. / Ruddock, L.W.
History
DepositionApr 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NHL repeat-containing protein 2
B: NHL repeat-containing protein 2
C: NHL repeat-containing protein 2
D: NHL repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)255,2174
Polymers255,2174
Non-polymers00
Water66737
1
A: NHL repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)63,8041
Polymers63,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NHL repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)63,8041
Polymers63,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NHL repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)63,8041
Polymers63,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NHL repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)63,8041
Polymers63,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.284, 103.812, 114.978
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 9 - 572 / Label seq-ID: 16 - 579

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
NHL repeat-containing protein 2


Mass: 63804.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHLRC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NBF2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BisTris Propane pH 6.5, 0.2 M K/Na Tartrate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.7→47.77 Å / Num. obs: 65063 / % possible obs: 98.9 % / Redundancy: 4.719 % / Biso Wilson estimate: 58.45 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.147 / Χ2: 0.982 / Net I/σ(I): 8.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.774.8921.0881.2948520.511.2299.5
2.77-2.854.9360.8441.7346700.6640.94699.7
2.85-2.934.8660.7362.0345950.6960.82699.8
2.93-3.024.8320.5642.6844360.8180.63499.6
3.02-3.124.8090.4473.4143270.8690.50399.6
3.12-3.234.7510.3684.1841560.9030.41699.6
3.23-3.354.7260.2695.6640080.9490.30498.6
3.35-3.484.7220.2127.2138410.9670.23998.9
3.48-3.644.6330.1858.1636460.9720.2198.9
3.64-3.824.5390.1569.5535310.9750.17898.5
3.82-4.024.3060.11611.8332940.9830.13397.2
4.02-4.273.8490.08513.7929680.9890.192.4
4.27-4.564.6190.07217.5729800.9930.08298.2
4.56-4.934.8930.06919.1428280.9950.07899.8
4.93-5.44.930.07318.3725980.9940.081100
5.4-6.044.8970.07417.7623540.9940.08399.9
6.04-6.974.8970.07218.2620860.9930.08199.6
6.97-8.544.7830.05820.7917570.9950.065100
8.54-12.074.6750.04725.0513740.9960.05399.1
12.07-47.774.3310.04324.587620.9970.04996.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HYX

2hyx


Resolution: 2.7→47.77 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.877 / SU B: 22.823 / SU ML: 0.436 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.416
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2872 3254 5 %RANDOM
Rwork0.2459 ---
obs0.248 61810 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 174.03 Å2 / Biso mean: 62.64 Å2 / Biso min: 19.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å21.16 Å2
2--1.95 Å20 Å2
3----1.84 Å2
Refinement stepCycle: final / Resolution: 2.7→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17018 0 0 37 17055
Biso mean---36.08 -
Num. residues----2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01517387
X-RAY DIFFRACTIONr_bond_other_d0.0020.01715839
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.73223598
X-RAY DIFFRACTIONr_angle_other_deg0.6521.70437116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.77252182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03321.544544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.045152573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1611556
X-RAY DIFFRACTIONr_chiral_restr0.0540.22271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119351
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023113
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A171880.08
12B171880.08
21A172260.08
22C172260.08
31A173170.07
32D173170.07
41B171470.08
42C171470.08
51B171390.08
52D171390.08
61C171590.08
62D171590.08
LS refinement shellResolution: 2.699→2.769 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 242 -
Rwork0.356 4597 -
all-4839 -
obs--99.55 %

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