[English] 日本語
Yorodumi
- PDB-4htg: Porphobilinogen Deaminase from Arabidopsis Thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4htg
TitlePorphobilinogen Deaminase from Arabidopsis Thaliana
ComponentsPorphobilinogen deaminase, chloroplastic
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Type-II periplasmic binding protein fold / Porphyrin binding / Tetrapyrrole biosynthesis / Porphobilinogen (porphyrin) binding / Chloroplast / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


peptidyl-pyrromethane cofactor linkage / chloroplast RNA modification / hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / chlorophyll biosynthetic process / protoporphyrinogen IX biosynthetic process / apoplast / chloroplast envelope / heme biosynthetic process / chloroplast stroma ...peptidyl-pyrromethane cofactor linkage / chloroplast RNA modification / hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / chlorophyll biosynthetic process / protoporphyrinogen IX biosynthetic process / apoplast / chloroplast envelope / heme biosynthetic process / chloroplast stroma / chloroplast / defense response to bacterium / plasma membrane / cytoplasm
Similarity search - Function
Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase / Porphobilinogen deaminase, N-terminal / Porphobilinogen deaminase, C-terminal / Porphobilinogen deaminase, dipyrromethane cofactor binding site / Porphobilinogen deaminase, C-terminal domain superfamily / Porphobilinogen deaminase, dipyromethane cofactor binding domain / Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase cofactor-binding site. / Double Stranded RNA Binding Domain ...Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase / Porphobilinogen deaminase, N-terminal / Porphobilinogen deaminase, C-terminal / Porphobilinogen deaminase, dipyrromethane cofactor binding site / Porphobilinogen deaminase, C-terminal domain superfamily / Porphobilinogen deaminase, dipyromethane cofactor binding domain / Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase cofactor-binding site. / Double Stranded RNA Binding Domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-18W / ACETATE ION / Porphobilinogen deaminase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRoberts, A. / Gill, R. / Hussey, R.J. / Erskine, P.T. / Cooper, J.B. / Wood, S.P. / Chrystal, E.J.T. / Shoolingin-Jordan, P.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme.
Authors: Roberts, A. / Gill, R. / Hussey, R.J. / Mikolajek, H. / Erskine, P.T. / Cooper, J.B. / Wood, S.P. / Chrystal, E.J. / Shoolingin-Jordan, P.M.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Porphobilinogen deaminase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1513
Polymers34,6581
Non-polymers4932
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Porphobilinogen deaminase, chloroplastic
hetero molecules

A: Porphobilinogen deaminase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3036
Polymers69,3162
Non-polymers9874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1870 Å2
ΔGint-7 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.573, 37.271, 55.069
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Porphobilinogen deaminase, chloroplastic / PBG / Hydroxymethylbilane synthase / HMBS / Pre-uroporphyrinogen synthase


Mass: 34657.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g08280, F8L15_10, HEMC / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q43316, hydroxymethylbilane synthase
#2: Chemical ChemComp-18W / 3-[(5Z)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methylidene}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid


Mass: 434.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O9
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5 mg/ml protein added in 50:50 ratio to the well-solution of 25% PEG 4000, 100 mM sodium citrate, 200 mM ammonium sulphate. Crystals grown in the dark due to photosensitivity of the cofactor. ...Details: 5 mg/ml protein added in 50:50 ratio to the well-solution of 25% PEG 4000, 100 mM sodium citrate, 200 mM ammonium sulphate. Crystals grown in the dark due to photosensitivity of the cofactor., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→32.89 Å / Num. obs: 49235 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7129 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDA

1pda


Resolution: 1.45→32.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.992 / SU ML: 0.052 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: REFMAC using riding hydrogens, anisotropic B-factors and each of the three protein domains as a separate TLS group.
RfactorNum. reflection% reflectionSelection details
Rfree0.21707 2455 5 %RANDOM
Rwork0.14495 ---
obs0.14859 46662 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.927 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.1 Å2
2---0.55 Å20 Å2
3---0.26 Å2
Refine analyzeLuzzati sigma a obs: 0.04 Å
Refinement stepCycle: LAST / Resolution: 1.45→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 35 409 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0522.0073254
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96724.19493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46515444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7941517
X-RAY DIFFRACTIONr_chiral_restr0.1350.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211774
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr6.3632405
X-RAY DIFFRACTIONr_sphericity_free38.3085149
X-RAY DIFFRACTIONr_sphericity_bonded19.63952627
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 164 -
Rwork0.264 3206 -
obs--96.64 %
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)
10.006-0.0014-0.00440.002-0.00140.00690.00090.00020.0007-0.0004-0.00010.0002-0.00030.0021-0.00080.0022-0.0002-0.00110.021800.0049-39.6133-7.046814.1149
20.0207-0.01160.01410.0149-0.01210.0185-0.0018-0.00330.0021-0.00110.002-0.0013-0.0022-0.0009-0.00020.00170.0002-0.00080.022200.0048-22.0566-0.862731.9124
30.00990.00120.00740.00020.00060.00660.00030.00090.00270.0003-0.00050.00070.00030.00270.00010.00230.0001-0.00080.0224-0.00070.0045-16.8653-13.691215.0597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 110
2X-RAY DIFFRACTION1A212 - 229
3X-RAY DIFFRACTION2A111 - 211
4X-RAY DIFFRACTION3A230 - 311

+
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