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- PDB-2ho4: Crystal Structure of Protein from Mouse Mm.236127 -

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Basic information

Entry
Database: PDB / ID: 2ho4
TitleCrystal Structure of Protein from Mouse Mm.236127
ComponentsHaloacid dehalogenase-like hydrolase domain containing 2
KeywordsHYDROLASE / Haloacid dehalogenase-like hydrolase domain containing 2 / Hdhd2 / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


phosphatase activity / enzyme binding / metal ion binding
Similarity search - Function
HAD hydrolase, LHPP/HDHD2 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Haloacid dehalogenase-like hydrolase domain-containing protein 2 / Haloacid dehalogenase-like hydrolase domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.2 Å
AuthorsMcCoy, J.G. / Wesenberg, G.E. / Bitto, E. / Phillips Jr., G.N. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: Crystal Structure of Protein from Mouse Mm.236127
Authors: McCoy, J.G. / WESENBERG, G.E. / BITTO, E. / PHILLIPS JR., G.N. / BINGMAN, C.A.
History
DepositionJul 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloacid dehalogenase-like hydrolase domain containing 2
B: Haloacid dehalogenase-like hydrolase domain containing 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,59410
Polymers57,9752
Non-polymers6188
Water2,396133
1
A: Haloacid dehalogenase-like hydrolase domain containing 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2975
Polymers28,9881
Non-polymers3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloacid dehalogenase-like hydrolase domain containing 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2975
Polymers28,9881
Non-polymers3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.586, 68.078, 190.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo monomers in the asymmetric unit (chains A & B)

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Components

#1: Protein Haloacid dehalogenase-like hydrolase domain containing 2


Mass: 28987.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hdhd2 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q6PEB2, UniProt: Q3UGR5*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K
Details: PROTEIN SOLUTION (10 MG/ML REDUCTIVELY METHYLATED PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (0. ...Details: PROTEIN SOLUTION (10 MG/ML REDUCTIVELY METHYLATED PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (0.3 M NaH2PO4, 1.7 M K2HPO4) AND CRYOPROTECTED WITH FOMBLIN FOLLOWED BY PARATONE N, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97929
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMETER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→46.5 Å / Num. obs: 30718 / % possible obs: 96.1 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.469
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.344 / % possible all: 73.4

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Phasing

PhasingMethod: MAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 2.2 Å / Lowest resolution: 41.87 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_100267123870
ANO_10.6881.558257830
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_19.59-41.8700257190
ISO_16.87-9.5900519191
ISO_15.64-6.8700704204
ISO_14.89-5.6400836196
ISO_14.38-4.8900967201
ISO_14-4.38001061194
ISO_13.71-4001182208
ISO_13.47-3.71001266197
ISO_13.27-3.47001349202
ISO_13.11-3.27001428189
ISO_12.96-3.11001524205
ISO_12.84-2.96001592205
ISO_12.73-2.84001648193
ISO_12.63-2.73001747205
ISO_12.54-2.63001803209
ISO_12.46-2.54001851192
ISO_12.39-2.46001901205
ISO_12.32-2.39001847186
ISO_12.26-2.32001707150
ISO_12.2-2.26001523148
ANO_19.59-41.870.4672.4922570
ANO_16.87-9.590.4312.8255190
ANO_15.64-6.870.3883.3547040
ANO_14.89-5.640.4313.048360
ANO_14.38-4.890.5062.6669660
ANO_14-4.380.5162.65510610
ANO_13.71-40.552.49811810
ANO_13.47-3.710.5312.4512660
ANO_13.27-3.470.5412.28813490
ANO_13.11-3.270.5871.99114270
ANO_12.96-3.110.6491.70215240
ANO_12.84-2.960.7391.38415920
ANO_12.73-2.840.7981.1416480
ANO_12.63-2.730.850.94917470
ANO_12.54-2.630.8990.79517960
ANO_12.46-2.540.9370.63818330
ANO_12.39-2.460.9590.49918340
ANO_12.32-2.390.9710.43716550
ANO_12.26-2.320.9850.37714170
ANO_12.2-2.260.9870.25711710
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-4.058-34.888-150.982SE48.181.65
2-6.415-53.362-125.385SE40.541.76
3-6.761-56.927-71.288SE46.441.66
4-3.854-42.207-0.331SE85.791.56
5-9.42-37.639-151.781SE39.741.53
6-1.226-38.68-135.828SE46.371.05
7-7.011-37.198-0.156SE60.561.39
8-1.071-10.144-128.34SE42.240.42
9-4.072-3.735-102.235SE66.751.25
10-5.609-3.585-76.774SE92.021.49
11-17.428-14.671-32.925SE55.740.13
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 30581
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.21-10072.80.617503
7.25-9.2166.70.868505
6.19-7.2561.60.834565
5.5-6.1960.80.858640
4.99-5.557.40.888714
4.61-4.9962.40.93748
4.3-4.6156.90.924829
4.04-4.361.50.901878
3.83-4.0460.50.905920
3.64-3.8361.80.892968
3.49-3.6462.10.8841012
3.35-3.4962.70.8781034
3.22-3.3563.10.8561093
3.11-3.2264.60.841099
3.01-3.1166.10.8361201
2.92-3.0163.50.8321174
2.83-2.9267.50.81244
2.76-2.83710.8141241
2.69-2.7669.30.791321
2.62-2.6970.30.8081309
2.56-2.6273.70.7981377
2.5-2.5673.20.7931370
2.45-2.5780.7871411
2.4-2.45790.7731464
2.35-2.479.70.7851379
2.31-2.3584.80.7731400
2.27-2.3183.70.7521276
2.2-2.27850.6861906

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.685 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1546 5.044 %RANDOM
Rwork0.224 ---
obs0.227 30651 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.786 Å20 Å20 Å2
2--0.354 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 32 133 4103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9985473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7585503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17924.689177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58615717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7821524
X-RAY DIFFRACTIONr_chiral_restr0.1110.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022992
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21866
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22715
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.52615
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3224064
X-RAY DIFFRACTIONr_scbond_it2.29131594
X-RAY DIFFRACTIONr_scangle_it3.3234.51407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 83 -
Rwork0.267 1566 -
obs--71.08 %

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