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- PDB-2qmq: Crystal structure of a n-myc downstream regulated 2 protein (ndrg... -

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Basic information

Entry
Database: PDB / ID: 2qmq
TitleCrystal structure of a n-myc downstream regulated 2 protein (ndrg2, syld, ndr2, ai182517, au040374) from mus musculus at 1.70 A resolution
ComponentsProtein NDRG2
KeywordsSIGNALING PROTEIN / Alpha/beta-hydrolases fold / ndr family / developmental protein / differentiation / neurogenesis / phosphorylation / regulatory protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / postsynapse organization / negative regulation of cytokine production / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / nervous system development / growth cone / cell differentiation ...regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / postsynapse organization / negative regulation of cytokine production / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / nervous system development / growth cone / cell differentiation / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleus / cytoplasm
Similarity search - Function
Protein NDRG2 / 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
BENZOIC ACID / Protein NDRG2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor.
Authors: Hwang, J. / Kim, Y. / Kang, H.B. / Jaroszewski, L. / Deacon, A.M. / 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 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 40-313 OF THE FULL LENGTH PROTEIN. IT WAS EXPRESSED ... SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 40-313 OF THE FULL LENGTH PROTEIN. IT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NDRG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5955
Polymers32,0101
Non-polymers5854
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.371, 46.371, 214.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Protein NDRG2 / Protein Ndr2


Mass: 32010.188 Da / Num. of mol.: 1 / Fragment: Residues 40-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: 15277975, Ndrg2, Kiaa1248, Ndr2 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9QYG0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 277 K / pH: 7.5
Details: NANODROP, 20.0% PEG 400, 0.2M MgCl2, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019976
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2005
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.019976 Å / Relative weight: 1
ReflectionResolution: 1.7→29.348 Å / Num. obs: 28650 / % possible obs: 92.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.405 / % possible all: 61.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U2E

1u2e


Resolution: 1.7→29.348 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.438 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MG AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION CONDITIONS. 4. THE BENZOIC ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MG AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION CONDITIONS. 4. THE BENZOIC ACID (BEZ) MOLECULE IS ASSIGNED BASED ON THE ELECTRON DENSITY AND ITS INTERACTION WITH THE PROTEIN. IT COULD BE SOME RELATED COMPOUND WITH A SIMILAR STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1449 5.1 %RANDOM
Rwork0.145 ---
obs0.147 28649 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 27 314 2493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222304
X-RAY DIFFRACTIONr_bond_other_d0.0080.021525
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9683151
X-RAY DIFFRACTIONr_angle_other_deg0.95333758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56825104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74115363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.224157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined0.2230.2469
X-RAY DIFFRACTIONr_nbd_other0.1930.21583
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21128
X-RAY DIFFRACTIONr_nbtor_other0.0870.21160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.45421522
X-RAY DIFFRACTIONr_mcbond_other0.4022572
X-RAY DIFFRACTIONr_mcangle_it1.97732313
X-RAY DIFFRACTIONr_scbond_it2.7514964
X-RAY DIFFRACTIONr_scangle_it3.7425826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 69 -
Rwork0.189 1302 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 3.7832 Å / Origin y: 34.5458 Å / Origin z: 16.8449 Å
111213212223313233
T-0.0432 Å2-0.0243 Å2-0.004 Å2--0.0141 Å20.0002 Å2---0.0311 Å2
L0.7468 °20.2506 °20.1012 °2-0.5567 °20.1081 °2--0.6603 °2
S0.013 Å °-0.1019 Å °-0.0032 Å °0.0357 Å °-0.0449 Å °-0.0177 Å °0.036 Å °0.0075 Å °0.0319 Å °

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