[English] 日本語
Yorodumi
- PDB-3zx4: The 3-dimensional structure of MpgP from Thermus thermophilus HB2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zx4
TitleThe 3-dimensional structure of MpgP from Thermus thermophilus HB27, in complex with the alpha-mannosylglycerate,orthophosphate and magnesium
ComponentsMANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
KeywordsHYDROLASE / HALOALKANOID ACID DEHALOGENASE-LIKE PHOSPHATASE / HAD-LIKE PHOSPHATASE / CRYSTALLOGRAPHIC SNAPSHOT
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity / mannosylglycerate biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
Mannosyl-3-phosphoglycerate phosphatase, thermophiles / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Mannosyl-3-phosphoglycerate phosphatase, thermophiles / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2M8 / PHOSPHATE ION / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGoncalves, S. / Esteves, A.M. / Santos, H. / Borges, N. / Matias, P.M.
Citation
Journal: Biochemistry / Year: 2011
Title: The Three-Dimensional Structure of Mannosyl-3-Phosphoglycerate Phosphatase from Thermus Thermophilus Hb27: A New Member of the Haloalkanoic Acid Dehalogenase Superfamily.
Authors: Goncalves, S. / Esteves, A.M. / Santos, H. / Borges, N. / Matias, P.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and Preliminary X-Ray Analysis of Mannosyl-3-Phosphoglycerate Phosphatase from Thermus Thermophilus Hb27.
Authors: Goncalves, S. / Esteves, A.M. / Borges, N. / Santos, H. / Matias, P.M.
History
DepositionAug 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
B: MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2148
Polymers56,4392
Non-polymers7756
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-44.6 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.900, 70.740, 92.300
Angle α, β, γ (deg.)90.00, 95.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.81677, 0.00794, 0.57691), (-0.01318, -0.99939, 0.03241), (0.57682, -0.03407, -0.81616)
Vector: -3.98789, 110.62743, 14.01073)

-
Components

#1: Protein MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE / MPGP


Mass: 28219.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q72K29, mannosyl-3-phosphoglycerate phosphatase
#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.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Sugar ChemComp-2M8 / (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid / 2-O-ALPHA-MANNOSYL-D-GLYCERATE / (2R)-3-hydroxy-2-(alpha-D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(mannosyloxy)propanoic acid


Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details2-O-ALPHA-MANNOSYL-D-GLYCERATE (2M8)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.19 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE REMARK 1 REFERENCE ABOVE, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.252
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 3, 2011 / Details: BENT CYLINDRICAL MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.252 Å / Relative weight: 1
ReflectionResolution: 1.74→60 Å / Num. obs: 50839 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 26.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.81
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.06 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZTY

3zty


Resolution: 1.74→38.533 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 21.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 2592 5.1 %
Rwork0.1722 --
obs0.1746 50834 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.293 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2698 Å20 Å2-0.3435 Å2
2--2.8306 Å20 Å2
3----6.1004 Å2
Refinement stepCycle: LAST / Resolution: 1.74→38.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 48 445 4393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064143
X-RAY DIFFRACTIONf_angle_d1.025646
X-RAY DIFFRACTIONf_dihedral_angle_d13.4141618
X-RAY DIFFRACTIONf_chiral_restr0.066614
X-RAY DIFFRACTIONf_plane_restr0.005749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.80210.3062530.22534569X-RAY DIFFRACTION92
1.8021-1.87430.22942570.19714814X-RAY DIFFRACTION97
1.8743-1.95960.24282590.18984787X-RAY DIFFRACTION97
1.9596-2.06290.23012690.17574818X-RAY DIFFRACTION97
2.0629-2.19210.21562810.16894811X-RAY DIFFRACTION97
2.1921-2.36140.21362320.16564863X-RAY DIFFRACTION97
2.3614-2.5990.20642620.16574784X-RAY DIFFRACTION97
2.599-2.97490.2252530.17994824X-RAY DIFFRACTION97
2.9749-3.74760.21132590.16984887X-RAY DIFFRACTION98
3.7476-38.54280.20952670.15945085X-RAY DIFFRACTION100
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)
10.7757-0.1020.16760.20410.16810.65940.5861-0.3545-1.5894-0.6113-0.03350.25662.08110.41040.01520.90620.1477-0.25390.41190.05940.777836.621850.02-15.6096
21.36550.4243-0.87231.4029-0.86383.49330.0978-0.19390.00690.0657-0.1335-0.13240.03690.1815-00.065-0.0058-0.00010.14780.04670.223735.801562.05620.357
31.0691-0.5510.80561.3104-0.42572.32440.1997-0.052-0.136-0.2726-0.02630.41050.2441-0.7776-0.00010.1788-0.0418-0.00970.35710.07580.302521.17963.27812.626
42.7488-1.18471.56612.617-0.81372.92960.40770.396-0.6901-0.52640.19240.58150.7579-0.15010.00050.3418-0.0648-0.17230.25560.03990.420929.461559.2002-20.2886
51.90931.13450.11221.8913-0.64742.65550.0606-0.21220.14080.4921-0.1233-0.228-0.2780.3460.00010.3561-0.0304-0.04970.2350.00130.145223.244750.7443.6378
62.48861.0594-0.7342.9563-0.25423.3944-0.06090.20280.07010.0320.04190.1561-0.14780.115-00.1107-0.01-0.00880.14650.01610.145620.596349.441421.4019
71.78920.3616-0.19781.9970.05441.7696-0.035-0.19430.14970.22860.01140.3594-0.1116-0.40790.00020.4216-0.00960.03460.2637-0.0260.17779.368950.297544.9369
80.05420.04570.00930.03850.00790.0016-0.0039-0.3281-0.73680.80230.041-0.11690.4011-0.20250.0061.0232-0.25810.0611.1223-0.07990.46515.12551.024362.3831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:30)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 31:134)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 135:175)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 176:250)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:87)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 88:175)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 176:249)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 250:254)

+
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://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