[English] 日本語
Yorodumi
- PDB-2nxf: Crystal Structure of a dimetal phosphatase from Danio rerio LOC 393393 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nxf
TitleCrystal Structure of a dimetal phosphatase from Danio rerio LOC 393393
ComponentsPutative dimetal phosphatase
KeywordsMETAL BINDING PROTEIN / dinuclear metal center phosphatase / metalloprotein / metallophosphoesterase / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG / PSI-2
Function / homology
Function and homology information


CDP-glycerol diphosphatase / Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase / CDP-glycerol diphosphatase activity / Phosphate bond hydrolysis by NUDT proteins / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / manganese ion binding
Similarity search - Function
Manganese-dependent ADP-ribose/CDP-alcohol diphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / PHOSPHATE ION / Manganese-dependent ADP-ribose/CDP-alcohol diphosphatase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsBitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / McCoy, J.G. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal Structure of a dimetal phosphatase from Danio rerio LOC 393393
Authors: Bitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / McCoy, J.G. / Bingman, C.A.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative dimetal phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1927
Polymers36,7891
Non-polymers4036
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.584, 86.593, 157.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is a monomer

-
Components

#1: Protein Putative dimetal phosphatase


Mass: 36789.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: Dr.12833, LOC 393393 / Plasmid: PVP 16K / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q7T291
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M BisTris pH 7.0) mixed in a 1:1 ratio with the Well Solution (10.4% PEG 4K, 0.40 M ...Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M BisTris pH 7.0) mixed in a 1:1 ratio with the Well Solution (10.4% PEG 4K, 0.40 M sodium chloride, 0.10 M HEPES pH 7.5) Cryoprotected with: 15% PEG 8K, 0.30 M ammonium thiocyanate, 0.010 M sodium dihydrogen phosphate, 0.0005 M zinc sulfate, 0.10 M HEPPS pH 8.5 supplemented with up to 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97923, 0.96400
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.9641
ReflectionResolution: 1.7→48.276 Å / Num. obs: 47311 / % possible obs: 99.8 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.083 / Χ2: 1.027 / Net I/σ(I): 14.348
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.748.20.4313.07730770.86598.1
1.74-1.7810.30.39331440.84999.8
1.78-1.8312.30.35230910.86100
1.83-1.8913.60.3131210.935100
1.89-1.9514.40.24831160.97100
1.95-2.0214.70.20831251100
2.02-2.114.80.16931301.114100
2.1-2.1914.80.14731291.107100
2.19-2.3114.90.12531621.175100
2.31-2.4514.80.10631411.142100
2.45-2.6414.60.08931621.081100
2.64-2.9114.40.08531581.067100
2.91-3.3314.30.08132091.14499.9
3.33-4.1914.40.05531950.92699.9
4.19-8013.90.05133510.98799.6

-
Phasing

PhasingMethod: MAD
Phasing MAD set

Highest resolution: 2.2 Å / Lowest resolution: 42.63 Å

IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_10000198122297
ISO_20.7180.7421.6731.164198042292
ANO_10.52202.2520198060
ANO_20.70201.2320197980
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_19.6-42.630000197105
ISO_16.88-9.60000374114
ISO_15.64-6.880000503114
ISO_14.89-5.640000598114
ISO_14.38-4.890000698114
ISO_14-4.380000773111
ISO_13.71-40000829121
ISO_13.47-3.710000908112
ISO_13.27-3.470000965120
ISO_13.11-3.2700001026110
ISO_12.96-3.1100001060116
ISO_12.84-2.9600001151118
ISO_12.73-2.8400001184109
ISO_12.63-2.7300001234119
ISO_12.54-2.6300001261117
ISO_12.46-2.5400001326112
ISO_12.39-2.4600001374123
ISO_12.32-2.3900001394114
ISO_12.26-2.3200001475114
ISO_12.2-2.2600001482120
ANO_19.6-42.630.46702.4401960
ANO_16.88-9.60.42102.84103740
ANO_15.64-6.880.35803.36605030
ANO_14.89-5.640.39903.07305980
ANO_14.38-4.890.5302.31706980
ANO_14-4.380.55902.20807730
ANO_13.71-40.52402.21208290
ANO_13.47-3.710.55202.17209080
ANO_13.27-3.470.50402.409650
ANO_13.11-3.270.50602.375010250
ANO_12.96-3.110.52602.263010580
ANO_12.84-2.960.49302.536011490
ANO_12.73-2.840.51302.286011840
ANO_12.63-2.730.52202.255012340
ANO_12.54-2.630.53402.194012610
ANO_12.46-2.540.56102.041013260
ANO_12.39-2.460.58201.782013740
ANO_12.32-2.390.60201.786013940
ANO_12.26-2.320.64101.618014750
ANO_12.2-2.260.68901.491014820
ISO_29.6-42.630.6770.682.1681.428196102
ISO_26.88-9.60.6850.6012.3671.921374114
ISO_25.64-6.880.6480.6042.5552.065503114
ISO_24.89-5.640.6680.722.2931.517598114
ISO_24.38-4.890.7330.8411.8031.104698114
ISO_24-4.380.7110.7411.6821.24773110
ISO_23.71-40.6920.7461.6561.159829121
ISO_23.47-3.710.6860.7321.6641.09908112
ISO_23.27-3.470.6830.7011.711.081965119
ISO_23.11-3.270.7070.7261.6381.0171026110
ISO_22.96-3.110.7110.7031.6741.1481060116
ISO_22.84-2.960.7390.8251.6930.891149118
ISO_22.73-2.840.7340.8051.650.9561184109
ISO_22.63-2.730.740.8531.5980.9551233119
ISO_22.54-2.630.7330.8051.5740.8651261117
ISO_22.46-2.540.7360.7351.470.8131324112
ISO_22.39-2.460.7440.8261.3560.8321374123
ISO_22.32-2.390.7540.7821.3160.7751394114
ISO_22.26-2.320.7580.7371.220.691475114
ISO_22.2-2.260.7880.8591.1350.6271480120
ANO_29.6-42.630.61601.48301960
ANO_26.88-9.60.54101.73703740
ANO_25.64-6.880.46502.24905030
ANO_24.89-5.640.53801.86405980
ANO_24.38-4.890.66601.42406980
ANO_24-4.380.6901.33707730
ANO_23.71-40.66701.29608290
ANO_23.47-3.710.68401.3609080
ANO_23.27-3.470.66301.32309650
ANO_23.11-3.270.70501.254010240
ANO_22.96-3.110.69301.334010590
ANO_22.84-2.960.68501.299011470
ANO_22.73-2.840.6901.271011830
ANO_22.63-2.730.71901.14012330
ANO_22.54-2.630.75901.097012610
ANO_22.46-2.540.76801013240
ANO_22.39-2.460.77700.931013740
ANO_22.32-2.390.82400.86013940
ANO_22.26-2.320.83200.803014750
ANO_22.2-2.260.88100.706014800
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
120.818-20.244-63.813SE19.521.1
219.564-19.37-57.214SE20.821.15
322.086-12.205-13.788SE29.21.2
426.488-28.204-10.743SE12.810.38
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 22109
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.03-100450.903504
6.32-8.0337.90.947506
5.5-6.3238.10.952512
4.97-5.540.20.95514
4.59-4.9740.20.965538
4.28-4.59420.967571
4.03-4.2842.50.961607
3.82-4.0344.50.954631
3.63-3.8246.30.956684
3.48-3.6343.90.962689
3.34-3.4846.30.955715
3.21-3.3445.90.942785
3.1-3.2145.10.95777
3-3.145.70.942818
2.91-344.20.938829
2.83-2.91500.927856
2.75-2.8348.50.931894
2.68-2.7548.40.924891
2.62-2.6849.10.923941
2.56-2.62500.922944
2.5-2.5651.60.917979
2.45-2.553.30.907992
2.4-2.45510.9161006
2.35-2.450.60.9161021
2.31-2.3554.70.9121058
2.26-2.3156.10.8811083
2.2-2.2658.90.841764

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→48.276 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.164 / SU B: 2.878 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2369 5.013 %RANDOM
Rwork0.161 ---
obs0.162 47258 99.728 %-
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: 27.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.338 Å20 Å20 Å2
2--0.711 Å20 Å2
3----1.048 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 12 354 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212647
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9313607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83723.172145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91515420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0091526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022099
X-RAY DIFFRACTIONr_nbd_refined0.1970.21267
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2285
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.215
X-RAY DIFFRACTIONr_mcbond_it0.711.51634
X-RAY DIFFRACTIONr_mcangle_it1.15622582
X-RAY DIFFRACTIONr_scbond_it2.02631131
X-RAY DIFFRACTIONr_scangle_it3.1384.51021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.7440.2771780.2313205348397.129
1.744-1.7920.2391910.23189338599.852
1.792-1.8440.2141730.1753141331699.94
1.844-1.9010.1991310.1643028316199.937
1.901-1.9630.1761600.15129293089100
1.963-2.0320.1951360.1512833297299.899
2.032-2.1090.1861220.1527912913100
2.109-2.1950.1641370.1552629276799.964
2.195-2.2920.1581550.14925422697100
2.292-2.4040.1631280.1522449257899.961
2.404-2.5340.171430.15922892432100
2.534-2.6870.1541010.1642211231399.957
2.687-2.8730.1731210.15220692190100
2.873-3.1020.18950.1631944204199.902
3.102-3.3980.1861030.1581767187199.947
3.398-3.7980.167820.1481638172199.942
3.798-4.3840.165620.14314591521100
4.384-5.3650.186770.1512301307100
5.365-7.570.233500.2189751025100
7.57-48.2760.133240.1957160598.347
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0926-0.3570.5280.87130.19222.65-0.02010.1233-0.1338-0.11130.0150.0840.2324-0.060.0051-0.11480.0073-0.0031-0.1757-0.0016-0.135626.007817.11469.4275
22.1784-1.21030.32932.6716-1.32353.10260.0608-0.09880.1575-0.01080.05120.1526-0.2337-0.186-0.112-0.14220.0331-0.0008-0.1492-0.0285-0.134723.11533.189821.0867
30.9147-0.0949-0.30890.67550.26942.71270.0083-0.07620.11330.00130.01-0.1646-0.07170.479-0.0183-0.13930.0196-0.0078-0.08620.0112-0.130538.992525.815219.7243
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
113 - 1143 - 114
22115 - 207115 - 207
33208 - 322208 - 322

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more