[English] 日本語
Yorodumi
- PDB-4mlm: Crystal Structure of PhnZ from uncultured bacterium HF130_AEPn_1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mlm
TitleCrystal Structure of PhnZ from uncultured bacterium HF130_AEPn_1
ComponentsPredicted HD phosphohydrolase PhnZ
KeywordsHYDROLASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / all alpha / carbon-phosphorus bond cleavage
Function / homology
Function and homology information


2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming) / oxidoreductase activity / hydrolase activity / metal ion binding
Similarity search - Function
HDIG domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / HD domain / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / L(+)-TARTARIC ACID / 2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming)
Similarity search - Component
Biological speciesuncultured bacterium HF130_AEPn_1 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
Authorsvan Staalduinen, L.M. / McSorley, F.R. / Zechel, D.L. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates.
Authors: van Staalduinen, L.M. / McSorley, F.R. / Schiessl, K. / Seguin, J. / Wyatt, P.B. / Hammerschmidt, F. / Zechel, D.L. / Jia, Z.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Predicted HD phosphohydrolase PhnZ
B: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,57813
Polymers45,4552
Non-polymers1,12311
Water6,774376
1
A: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2747
Polymers22,7281
Non-polymers5466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3056
Polymers22,7281
Non-polymers5775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-94 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.670, 76.040, 60.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-356-

HOH

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Predicted HD phosphohydrolase PhnZ


Mass: 22727.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium HF130_AEPn_1 (environmental samples)
Gene: ALOHA_HF130_AEPn_1_06c / Plasmid: pJExpress / Production host: Escherichia coli (E. coli) / References: UniProt: D0E8I5
#6: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 6 types, 386 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.4 M ammonium sulfate, 0.15 M potassium sodium L-tartrate, 0.5 % n-octyl-beta,D-glucoside, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794, 0.9796, 0.9778
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2011
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.97781
ReflectionResolution: 1.7→19.8 Å / Num. all: 102392 / Num. obs: 103003 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.057
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 14.4 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
autoSHARPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.8 Å / SU ML: 0.21 / σ(F): 1.47 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 2744 5.08 %RANDOM
Rwork0.1717 ---
obs0.173 53980 99.97 %-
all-53980 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.453 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1688 Å20 Å2-0 Å2
2--0.3704 Å20 Å2
3----0.2017 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 61 376 3426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093157
X-RAY DIFFRACTIONf_angle_d0.9414254
X-RAY DIFFRACTIONf_dihedral_angle_d13.0011190
X-RAY DIFFRACTIONf_chiral_restr0.068439
X-RAY DIFFRACTIONf_plane_restr0.003551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.27361410.24682527X-RAY DIFFRACTION100
1.7293-1.76070.27411560.21562483X-RAY DIFFRACTION100
1.7607-1.79460.21421130.21652560X-RAY DIFFRACTION100
1.7946-1.83120.23081230.20662553X-RAY DIFFRACTION100
1.8312-1.8710.23691480.2022515X-RAY DIFFRACTION100
1.871-1.91450.25331280.19282525X-RAY DIFFRACTION100
1.9145-1.96230.1981190.17992572X-RAY DIFFRACTION100
1.9623-2.01530.25271360.1722530X-RAY DIFFRACTION100
2.0153-2.07460.21031590.17112503X-RAY DIFFRACTION100
2.0746-2.14140.19881380.1632522X-RAY DIFFRACTION100
2.1414-2.21790.18831370.16112558X-RAY DIFFRACTION100
2.2179-2.30660.19021130.16262591X-RAY DIFFRACTION100
2.3066-2.41140.21421500.15562511X-RAY DIFFRACTION100
2.4114-2.53830.20451490.16532585X-RAY DIFFRACTION100
2.5383-2.69690.18441280.17032573X-RAY DIFFRACTION100
2.6969-2.90460.19671400.16642561X-RAY DIFFRACTION100
2.9046-3.19580.18611570.16892572X-RAY DIFFRACTION100
3.1958-3.65570.16091190.15792612X-RAY DIFFRACTION100
3.6557-4.59630.15151430.14382629X-RAY DIFFRACTION100
4.5963-19.81970.2231470.19762754X-RAY DIFFRACTION100

+
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