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- PDB-6g7w: Crystal structure of NHL repeat containing domain of human NHLRC2 -

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Basic information

Entry
Database: PDB / ID: 6g7w
TitleCrystal structure of NHL repeat containing domain of human NHLRC2
ComponentsNHL repeat-containing protein 2
KeywordsUNKNOWN FUNCTION / NHL repeat containing / structural domain / protein binding
Function / homology
Function and homology information


platelet alpha granule lumen / Platelet degranulation / extracellular region / cytosol
Similarity search - Function
NHL2, NHL repeat domain / Thioredoxin-like / NHL repeat profile. / NHL repeat / NHL repeat / Thioredoxin-like fold / Six-bladed beta-propeller, TolB-like / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NHL repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.746 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 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NHL repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)39,1111
Polymers39,1111
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.631, 46.491, 70.302
Angle α, β, γ (deg.)90.000, 102.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NHL repeat-containing protein 2


Mass: 39110.945 Da / Num. of mol.: 1
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.: 320 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Li2SO4, 0.1 M BisTris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.42→46.331 Å / Num. obs: 42106 / % possible obs: 67.5 % / Redundancy: 2.917 % / Biso Wilson estimate: 17.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.058 / Χ2: 1.036 / Net I/σ(I): 12.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.42-1.461.5581.0250.452600.3261.4395.7
1.46-1.51.8450.8140.677010.3321.12615.7
1.5-1.541.9080.6030.9210950.5090.83225.3
1.54-1.592.0540.4921.215570.6640.66436.6
1.59-1.642.2130.431.5618480.7370.56845.1
1.64-1.72.460.3442.1222050.8090.44155.9
1.7-1.772.6450.2762.8526400.8970.34669
1.77-1.842.9060.2094.0732480.9440.25688.5
1.84-1.923.1580.1565.9534630.9690.18898.1
1.92-2.013.0950.1197.7433500.980.14498
2.01-2.1230.0999.5830580.9860.12195.8
2.12-2.253.180.08311.8130030.9910.09998.5
2.25-2.413.1550.06914.0628240.9930.08398.4
2.41-2.63.110.06115.7926090.9940.07497.1
2.6-2.853.2830.0519.5924270.9960.0699.1
2.85-3.183.2210.03825.5822100.9980.04598.8
3.18-3.673.1960.02933.1719350.9980.03597.2
3.67-4.53.2080.02438.6116700.9990.02998.9
4.5-6.363.1540.02339.2212820.9990.02797.3
6.36-46.3312.9990.02240.457210.9990.02695.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.746→46.331 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.37
RfactorNum. reflection% reflection
Rfree0.1892 1630 5 %
Rwork0.1548 --
obs0.1565 32600 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.88 Å2 / Biso mean: 21.8647 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.746→46.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 0 320 2971
Biso mean---30.45 -
Num. residues----349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7459-1.79720.27321100.22442081219178
1.7972-1.85520.22831340.20262546268095
1.8552-1.92160.23561370.16172599273699
1.9216-1.99850.22731380.15992630276898
1.9985-2.08940.19331360.15672578271497
2.0894-2.19960.21691370.16282616275397
2.1996-2.33740.22251380.16232619275798
2.3374-2.51790.22791390.16382641278098
2.5179-2.77120.22971390.17322629276898
2.7712-3.17210.20391400.1642662280299
3.1721-3.99620.15511390.14112654279398
3.9962-46.34690.12531430.12392715285897
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)
12.0346-0.8137-0.69692.12030.43133.86210.0320.1366-0.0587-0.10540.0131-0.0070.0520.0934-0.03240.0838-0.0067-0.00570.09670.0060.116824.848628.3134.6399
22.53990.3376-0.61531.4587-0.77372.40680.00090.15750.0656-0.05440.05870.06050.0208-0.1817-0.05170.08570.0039-0.01730.104-0.00220.09718.60727.13029.095
32.8322-0.24640.2380.8355-0.25682.54390.0221-0.1099-0.28240.010.02420.06710.1581-0.171-0.04750.1343-0.02270.01230.11930.00840.14679.023914.700822.2819
41.98150.3499-0.83040.7959-0.4221.24870.0164-0.2314-0.08790.0657-0.075-0.08730.0240.15170.06390.1229-0.0009-0.0260.12360.01280.117329.4621.335222.2983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 220 through 262 )A220 - 262
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 370 )A263 - 370
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 451 )A371 - 451
4X-RAY DIFFRACTION4chain 'A' and (resid 452 through 572 )A452 - 572

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