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- PDB-2rh0: Crystal structure of NudC domain-containing protein 2 (13542905) ... -

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Basic information

Entry
Database: PDB / ID: 2rh0
TitleCrystal structure of NudC domain-containing protein 2 (13542905) from Mus musculus at 1.95 A resolution
ComponentsNudC domain-containing protein 2
KeywordsNUCLEAR PROTEIN / 13542905 / NudC domain-containing protein 2 / Nuclear movement protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


intercellular bridge / mitotic spindle / kinetochore / spindle pole / unfolded protein binding / protein folding / centrosome / cytosol / cytoplasm
Similarity search - Function
NudC domain-containing protein 2, p23 domain / Single helix bin / NudC family / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...NudC domain-containing protein 2, p23 domain / Single helix bin / NudC family / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NudC domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NudC domain-containing protein 2 (13542905) from Mus musculus at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CONSTRUCT CONTAINS RESIDUES 5-157 OF THE TARGET SEQUENCE. A C-TERMINAL FRAMESHIFT RESULTS IN SEQUENCE CHANGES FOR THE LAST TWO RESIDUES OF THE TARGET SEQUENCE (E156G AND K157N) AND THE PRESENCE OF THREE ADDITIONAL RESIDUES (158D, 159G, 160T) AT THE C-TERMINUS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NudC domain-containing protein 2
B: NudC domain-containing protein 2
C: NudC domain-containing protein 2
D: NudC domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7037
Polymers70,5174
Non-polymers1863
Water7,242402
1
A: NudC domain-containing protein 2
B: NudC domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3213
Polymers35,2592
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
MethodPISA
2
C: NudC domain-containing protein 2
D: NudC domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3834
Polymers35,2592
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.568, 64.504, 64.423
Angle α, β, γ (deg.)74.51, 81.06, 81.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / Refine code: 2

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERAA6 - 1373 - 134
2SERBB6 - 1373 - 134
3PHECC6 - 1363 - 133
4SERDD6 - 1373 - 134

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Components

#1: Protein
NudC domain-containing protein 2


Mass: 17629.301 Da / Num. of mol.: 4 / Fragment: Residues 5-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: 13542905, Nudcd2, D11Ertd603e / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9CQ48
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: NANODROP, 0.2M NaNO3, 20.0% PEG 3350, No Buffer pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.95→29.148 Å / Num. obs: 47221 / % possible obs: 95.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 3.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-22.90.6070.81009934500.60794.2
2-2.062.90.4981.3972333300.49894.7
2.06-2.122.90.4130.9964333150.41394.9
2.12-2.182.90.3162.1930031800.31694.9
2.18-2.252.90.2572.3905931080.25795.1
2.25-2.332.90.2442.7876029950.24495
2.33-2.422.90.1923.5856629260.19295.4
2.42-2.522.90.1763.7810327900.17695.6
2.52-2.632.90.1614.1789627030.16195.7
2.63-2.762.90.1295.2748025540.12995.7
2.76-2.912.90.116.1725224940.1196.1
2.91-3.082.90.0917.2668322980.09196.2
3.08-3.32.90.0768.7639121860.07696.1
3.3-3.562.90.06410.2592620410.06496.5
3.56-3.92.90.0610.2540418640.0696.3
3.9-4.362.90.0582.8495417190.05896.6
4.36-5.032.90.05112.5429914910.05196.8
5.03-6.172.80.0659.4357412630.06596.7
6.17-8.722.80.059827919880.05997
8.72-29.1482.80.068.214775260.0694.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→29.148 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.267 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.153
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO FROM THE CRYO SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2394 5.1 %RANDOM
Rwork0.19 ---
obs0.192 47101 95.33 %-
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: 28.349 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20.8 Å21.24 Å2
2---0.86 Å21.88 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 12 403 4642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224339
X-RAY DIFFRACTIONr_bond_other_d0.0020.022973
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9465899
X-RAY DIFFRACTIONr_angle_other_deg0.89637262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.19425.024207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27215753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7681526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02851
X-RAY DIFFRACTIONr_nbd_refined0.2140.2780
X-RAY DIFFRACTIONr_nbd_other0.1950.23062
X-RAY DIFFRACTIONr_nbtor_refined0.180.22081
X-RAY DIFFRACTIONr_nbtor_other0.0920.22369
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.214
X-RAY DIFFRACTIONr_mcbond_it2.6932914
X-RAY DIFFRACTIONr_mcbond_other0.29531080
X-RAY DIFFRACTIONr_mcangle_it3.50854294
X-RAY DIFFRACTIONr_scbond_it5.4981899
X-RAY DIFFRACTIONr_scangle_it7.946111593
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A759TIGHT POSITIONAL0.090.2
B759TIGHT POSITIONAL0.10
C759TIGHT POSITIONAL0.10
D759TIGHT POSITIONAL0.10
A920MEDIUM POSITIONAL0.31
B920MEDIUM POSITIONAL0.30
C920MEDIUM POSITIONAL0.280
D920MEDIUM POSITIONAL0.330
A759TIGHT THERMAL0.150.5
B759TIGHT THERMAL0.170
C759TIGHT THERMAL0.160
D759TIGHT THERMAL0.160
A920MEDIUM THERMAL0.132
B920MEDIUM THERMAL0.130
C920MEDIUM THERMAL0.130
D920MEDIUM THERMAL0.130
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 158 -
Rwork0.299 3200 -
all-3358 -
obs--92.18 %

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