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- PDB-2xms: Crystal structure of human NDRG2 protein provides insight into it... -

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Basic information

Entry
Database: PDB / ID: 2xms
TitleCrystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor
ComponentsPROTEIN NDRG2
KeywordsSIGNALING PROTEIN / NDRG FAMILY
Function / homology
Function and homology information


regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / vascular associated smooth muscle cell proliferation / negative regulation of cytokine production / negative regulation of vascular associated smooth muscle cell proliferation / substantia nigra development / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / growth cone / cell differentiation ...regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / vascular associated smooth muscle cell proliferation / negative regulation of cytokine production / negative regulation of vascular associated smooth muscle cell proliferation / substantia nigra development / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / growth cone / cell differentiation / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
NDRG / Ndr family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Protein NDRG2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHwang, J. / Kim, Y. / Lee, H. / Kim, M.H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Human Ndrg2 Protein Provides Insight Into its Role as a Tumor Suppressor.
Authors: Hwang, J. / Kim, Y. / Kang, H.B. / Jaroszewski, L. / Deacon, A. / Lee, H. / Choi, W.C. / Kim, K.J. / Kim, C.H. / Kang, B.S. / Lee, J.O. / Oh, T.K. / Kim, J.W. / Wilson, I.A. / Kim, M.H.
History
DepositionJul 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN NDRG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5794
Polymers31,4061
Non-polymers1743
Water2,468137
1
A: PROTEIN NDRG2
hetero molecules

A: PROTEIN NDRG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1588
Polymers62,8112
Non-polymers3476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2330 Å2
ΔGint-14.9 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.098, 93.098, 90.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

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Components

#1: Protein PROTEIN NDRG2 / NDRG2


Mass: 31405.525 Da / Num. of mol.: 1 / Fragment: ALPHA-BETA HYDROLASE DOMAIN, RESIDUES 24-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UN36
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growDetails: 1.5 M NACL AND 0.1 M IMIDAZOLE (PH 7.0 TO 8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 24942 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.16
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.78 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QMQ

2qmq


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.731 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1268 5.1 %RANDOM
Rwork0.17267 ---
obs0.1744 23642 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 11 137 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222284
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9633110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0155280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42324.86107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5615356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.007158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2988
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21560
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9951.51441
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35322271
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1413964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4344.5839
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.152→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 113 -
Rwork0.227 1686 -
obs--99.78 %

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