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- PDB-6zmm: Crystal structure of human NDRG1 -

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Basic information

Entry
Database: PDB / ID: 6zmm
TitleCrystal structure of human NDRG1
ComponentsProtein NDRG1
KeywordsLIPID BINDING PROTEIN / tumor suppressor / metal binding protein
Function / homology
Function and homology information


mast cell activation / peripheral nervous system myelin maintenance / gamma-tubulin binding / response to metal ion / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / DNA damage response, signal transduction by p53 class mediator / adherens junction / small GTPase binding / recycling endosome membrane / microtubule cytoskeleton ...mast cell activation / peripheral nervous system myelin maintenance / gamma-tubulin binding / response to metal ion / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / DNA damage response, signal transduction by p53 class mediator / adherens junction / small GTPase binding / recycling endosome membrane / microtubule cytoskeleton / microtubule binding / cellular response to hypoxia / microtubule / cadherin binding / negative regulation of cell population proliferation / centrosome / perinuclear region of cytoplasm / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NDRG / Ndr family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsMustonen, V. / Kursula, P. / Ruskamo, S.
Funding support Finland, 2items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
Academy of Finland Finland
CitationJournal: Febs J. / Year: 2021
Title: Crystal and solution structure of NDRG1, a membrane-binding protein linked to myelination and tumour suppression.
Authors: Mustonen, V. / Muruganandam, G. / Loris, R. / Kursula, P. / Ruskamo, S.
History
DepositionJul 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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

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Assembly

Deposited unit
A: Protein NDRG1
B: Protein NDRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4043
Polymers63,3682
Non-polymers351
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Monomeric protein in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-7 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.570, 108.570, 119.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTHRTHR(chain 'A' and (resid 32 through 168 or resid 185...AA32 - 512 - 21
12ARGARGCYSCYS(chain 'A' and (resid 32 through 168 or resid 185...AA56 - 16826 - 138
13GLNGLNPHEPHE(chain 'A' and (resid 32 through 168 or resid 185...AA185 - 196155 - 166
14VALVALARGARG(chain 'A' and (resid 32 through 168 or resid 185...AA207 - 241177 - 211
15VALVALPROPRO(chain 'A' and (resid 32 through 168 or resid 185...AA249 - 316219 - 286
26VALVALTHRTHR(chain 'B' and (resid 32 through 51 or resid 56...BB32 - 512 - 21
27ARGARGCYSCYS(chain 'B' and (resid 32 through 51 or resid 56...BB56 - 16826 - 138
28GLNGLNPHEPHE(chain 'B' and (resid 32 through 51 or resid 56...BB185 - 196155 - 166
29VALVALARGARG(chain 'B' and (resid 32 through 51 or resid 56...BB207 - 241177 - 211
210VALVALPROPRO(chain 'B' and (resid 32 through 51 or resid 56...BB249 - 316219 - 286

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Components

#1: Protein Protein NDRG1 / Differentiation-related gene 1 protein / DRG-1 / N-myc downstream-regulated gene 1 protein / Nickel- ...Differentiation-related gene 1 protein / DRG-1 / N-myc downstream-regulated gene 1 protein / Nickel-specific induction protein Cap43 / Reducing agents and tunicamycin-responsive protein / RTP / Rit42


Mass: 31684.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDRG1, CAP43, DRG1, RTP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92597
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / Details: 1.4 M sodium malonate (pH 6.25), 10 mM TCEP

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.96→48.55 Å / Num. obs: 14800 / % possible obs: 95.66 % / Redundancy: 4.26 % / Biso Wilson estimate: 63.71 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.33
Reflection shellResolution: 2.96→3.07 Å / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1405 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XMQ

2xmq


Resolution: 2.96→48.55 Å / SU ML: 0.5121 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2946 733 4.98 %
Rwork0.2685 14000 -
obs0.2699 14733 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.42 Å2
Refinement stepCycle: LAST / Resolution: 2.96→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 1 12 3874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233942
X-RAY DIFFRACTIONf_angle_d0.57655355
X-RAY DIFFRACTIONf_chiral_restr0.0454610
X-RAY DIFFRACTIONf_plane_restr0.0035702
X-RAY DIFFRACTIONf_dihedral_angle_d18.03221435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.190.44571410.37932695X-RAY DIFFRACTION93.91
3.19-3.510.30111470.29532812X-RAY DIFFRACTION98.11
3.51-4.020.27611490.25842820X-RAY DIFFRACTION97.86
4.02-5.060.26481430.23092768X-RAY DIFFRACTION94.67
5.07-48.550.28331530.25882905X-RAY DIFFRACTION94.18

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