[English] 日本語
Yorodumi
- PDB-2p10: CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p10
TitleCRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9387) FROM MESORHIZOBIUM LOTI MAFF303099 AT 2.15 A RESOLUTION
ComponentsMll9387 protein
KeywordsHYDROLASE / PUTATIVE PHOSPHONOPYRUVATE HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


TIM-barrel domain, IGPS-like / Phosphoenolpyruvate hydrolase-like / Single helix bin / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle ...TIM-barrel domain, IGPS-like / Phosphoenolpyruvate hydrolase-like / Single helix bin / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Mll9387 protein
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_085906.1) from Mesorhizobium loti at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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, FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mll9387 protein
B: Mll9387 protein
C: Mll9387 protein
D: Mll9387 protein
E: Mll9387 protein
F: Mll9387 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,21229
Polymers186,8636
Non-polymers1,34923
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29970 Å2
ΔGint-256 kcal/mol
Surface area53030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.269, 180.269, 185.514
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 9 - 283 / Label seq-ID: 10 - 284

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

-
Components

#1: Protein
Mll9387 protein


Mass: 31143.910 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: NP_085906.1, mll9387 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q981G2
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 277 K / pH: 4
Details: NANODROP, 3.0% PEG 4000, 23.3% Glycerol, 0.1M Sodium acetate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381, 0.979354
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2007
Details: 1M LONG RH COATED BENT CYLINDRICAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.9793541
ReflectionResolution: 2.15→45.083 Å / Num. obs: 121425 / % possible obs: 99.3 % / Redundancy: 3.31 % / Biso Wilson estimate: 37.31 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.34
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2.15-2.233.280.7641.641411199.6
2.23-2.320.618240111199.6
2.32-2.420.4852.538189199.7
2.42-2.550.3743.240952199.6
2.55-2.710.2884.240354199.6
2.71-2.920.196640561199.5
2.92-3.210.1248.940003199.6
3.21-3.670.06913.840334199.4
3.67-4.610.04419.440328199.2
4.61-45.10.0421.939992197.5

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→45.08 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.716 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. ACETATE, GLYCEROL AND CHLORIDE ATOMS, PRESENT IN THE CRYSTALLIZATION SOLUTION, ARE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 6092 5 %RANDOM
Rwork0.162 ---
obs0.165 121409 99.3 %-
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: 43.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12016 0 82 712 12810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212412
X-RAY DIFFRACTIONr_bond_other_d0.0010.028478
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.97816760
X-RAY DIFFRACTIONr_angle_other_deg0.888320648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55651639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70823.448522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.134152121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.37615108
X-RAY DIFFRACTIONr_chiral_restr0.0670.21901
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022482
X-RAY DIFFRACTIONr_nbd_refined0.2050.22787
X-RAY DIFFRACTIONr_nbd_other0.1890.29308
X-RAY DIFFRACTIONr_nbtor_refined0.1720.26218
X-RAY DIFFRACTIONr_nbtor_other0.0860.26601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2624
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1180.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.40438290
X-RAY DIFFRACTIONr_mcbond_other0.46833325
X-RAY DIFFRACTIONr_mcangle_it2.283512819
X-RAY DIFFRACTIONr_scbond_it4.78984573
X-RAY DIFFRACTIONr_scangle_it6.594113920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1533medium positional0.190.5
2B1533medium positional0.180.5
3C1533medium positional0.210.5
4D1533medium positional0.180.5
5E1533medium positional0.20.5
6F1533medium positional0.30.5
1A1618loose positional0.435
2B1618loose positional0.465
3C1618loose positional0.585
4D1618loose positional0.455
5E1618loose positional0.55
6F1618loose positional0.565
1A1533medium thermal0.962
2B1533medium thermal0.772
3C1533medium thermal0.882
4D1533medium thermal0.732
5E1533medium thermal0.722
6F1533medium thermal0.632
1A1618loose thermal2.7310
2B1618loose thermal2.310
3C1618loose thermal2.4910
4D1618loose thermal2.2310
5E1618loose thermal2.510
6F1618loose thermal2.4310
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 433 -
Rwork0.283 8561 -
obs--99.38 %
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)
10.31240.2759-0.14920.7175-0.54220.80570.05480.0780.0571-0.0173-0.0636-0.0869-0.09440.14290.0088-0.05170.01590.0419-0.06170.0411-0.098817.22339.3448.379
20.5818-0.446-0.12971.0584-0.04230.3261-0.0937-0.022-0.18180.00240.05160.16370.1167-0.0260.0421-0.0939-0.02450.0203-0.10330.0316-0.06660.59962.585-19.634
30.7805-0.09190.47291.6135-0.77841.58720.0731-0.09730.12890.41610.17120.6441-0.1428-0.291-0.24440.08520.02940.269-0.06160.10260.2871-16.29659.53916.409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 2849 - 285
2X-RAY DIFFRACTION1BB9 - 28510 - 286
3X-RAY DIFFRACTION2CC9 - 28410 - 285
4X-RAY DIFFRACTION2DD9 - 28410 - 285
5X-RAY DIFFRACTION3EE9 - 28310 - 284
6X-RAY DIFFRACTION3FF9 - 28310 - 284

+
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