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- PDB-6l4b: Crystal structure of human WT NDRG3 -

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Basic information

Entry
Database: PDB / ID: 6l4b
TitleCrystal structure of human WT NDRG3
ComponentsProtein NDRG3
KeywordsSIGNALING PROTEIN / alpha/beta-hydrolase fold / NDRG3 / Unfolded helix
Function / homology
Function and homology information


negative regulation of cell growth / spermatogenesis / cell differentiation / signal transduction / extracellular exosome / 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: 2.2 Å
AuthorsKim, K.R. / Han, B.W.
CitationJournal: Biomolecules / Year: 2020
Title: Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein.
Authors: Kim, K.R. / Kim, K.A. / Park, J.S. / Jang, J.Y. / Choi, Y. / Lee, H.H. / Lee, D.C. / Park, K.C. / Yeom, Y.I. / Kim, H.J. / Han, B.W.
History
DepositionOct 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Data collection / Category: pdbx_reflns_twin / Item: _pdbx_reflns_twin.diffrn_id
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NDRG3
B: Protein NDRG3
E: Protein NDRG3
F: Protein NDRG3
C: Protein NDRG3
D: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)248,6986
Polymers248,6986
Non-polymers00
Water5,747319
1
A: Protein NDRG3

E: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)82,8992
Polymers82,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2010 Å2
ΔGint-11 kcal/mol
Surface area24070 Å2
MethodPISA
2
B: Protein NDRG3
F: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)82,8992
Polymers82,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area24270 Å2
MethodPISA
3
C: Protein NDRG3

D: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)82,8992
Polymers82,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area1960 Å2
ΔGint-10 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.341, 100.150, 110.744
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein NDRG3 / N-myc downstream-regulated gene 3 protein


Mass: 41449.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDRG3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGV2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 200 mM sodium citrate tribasic dehydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.1723
pseudo-merohedral21-h,-k,l20.1769
pseudo-merohedral31-1/2H-3/2K, -1/2H+1/2K, -L30.1945
pseudo-merohedral41-1/2H+3/2K, 1/2H+1/2K, -L40.1289
pseudo-merohedral511/2H+3/2K, 1/2H-1/2K, -L50.1311
pseudo-merohedral611/2H-3/2K, -1/2H-1/2K, -L60.1963
ReflectionResolution: 2.2→50 Å / Num. obs: 95796 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.641 / Num. unique obs: 4774

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XMQ

2xmq


Resolution: 2.2→46.671 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1848 4347 4.896 %
Rwork0.1677 --
all0.169 --
obs-88790 92.228 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.604 Å2
Baniso -1Baniso -2Baniso -3
1--3.683 Å2-0 Å2-19.234 Å2
2---5.101 Å2-0 Å2
3---8.784 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13134 0 0 319 13453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01313419
X-RAY DIFFRACTIONr_bond_other_d0.0360.01712210
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.63418252
X-RAY DIFFRACTIONr_angle_other_deg2.31.56728476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08451680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68224.386684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.791152208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1011548
X-RAY DIFFRACTIONr_chiral_restr0.040.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215066
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022526
X-RAY DIFFRACTIONr_nbd_refined0.1710.22864
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.211918
X-RAY DIFFRACTIONr_nbtor_refined0.1440.26471
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0620.25270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2498
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.260.269
X-RAY DIFFRACTIONr_nbd_other0.3060.2249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.220
X-RAY DIFFRACTIONr_mcbond_it0.8283.4576756
X-RAY DIFFRACTIONr_mcbond_other0.8283.4576755
X-RAY DIFFRACTIONr_mcangle_it1.5175.1788424
X-RAY DIFFRACTIONr_mcangle_other1.5165.1798425
X-RAY DIFFRACTIONr_scbond_it0.4273.486662
X-RAY DIFFRACTIONr_scbond_other0.4273.486662
X-RAY DIFFRACTIONr_scangle_it0.8135.2029828
X-RAY DIFFRACTIONr_scangle_other0.8125.2029829
X-RAY DIFFRACTIONr_lrange_it3.16241.32814684
X-RAY DIFFRACTIONr_lrange_other3.15541.33114669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2560.2762330.2394227X-RAY DIFFRACTION62.8435
2.256-2.3180.2642470.2334698X-RAY DIFFRACTION71.5009
2.318-2.3850.3272380.2225013X-RAY DIFFRACTION78.4551
2.385-2.4580.3342430.2415373X-RAY DIFFRACTION86.2805
2.458-2.5380.2592730.235684X-RAY DIFFRACTION94.0926
2.538-2.6270.3612640.235761X-RAY DIFFRACTION98.496
2.627-2.7260.22800.2015530X-RAY DIFFRACTION99.3502
2.726-2.8370.2362470.1875437X-RAY DIFFRACTION100.2469
2.837-2.9630.1583130.1795203X-RAY DIFFRACTION100.0181
2.963-3.1070.2122660.1634942X-RAY DIFFRACTION99.8658
3.107-3.2740.192180.1724742X-RAY DIFFRACTION99.9798
3.274-3.4720.1612520.1594533X-RAY DIFFRACTION100.0418
3.472-3.710.1641830.1384203X-RAY DIFFRACTION100.2973
3.71-4.0060.1122160.1253885X-RAY DIFFRACTION99.3459
4.006-4.3850.1212080.1293595X-RAY DIFFRACTION100.1316
4.385-4.8980.1511740.1213235X-RAY DIFFRACTION100
4.898-5.6470.1411760.152899X-RAY DIFFRACTION99.9025
5.647-6.8940.2181010.1652500X-RAY DIFFRACTION100.077
6.894-9.6580.1951250.1291908X-RAY DIFFRACTION99.7057
9.658-46.6710.134900.1841075X-RAY DIFFRACTION97.653

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