[English] 日本語
Yorodumi
- PDB-2pnj: Crystal structure of human ferrochelatase mutant with Phe 337 rep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pnj
TitleCrystal structure of human ferrochelatase mutant with Phe 337 replaced by Ala
ComponentsFerrochelatase, mitochondrial
KeywordsLYASE / FERROCHELATASE / F337A Mutant / FE2S2 CLUSTER / HEME BIOSYNTHESIS / PROTOHEME FERRO-LYASE / MATURE LENGTH / PROTEOLYTICALLY PROCESSED MITOCHONDRIAL INNER MEMBRANE PROTEIN
Function / homology
Function and homology information


protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / detection of UV / iron-responsive element binding / response to platinum ion / response to insecticide / protoporphyrin ferrochelatase / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process ...protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / detection of UV / iron-responsive element binding / response to platinum ion / response to insecticide / protoporphyrin ferrochelatase / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / ferrochelatase activity / very-low-density lipoprotein particle assembly / response to methylmercury / response to arsenic-containing substance / Heme biosynthesis / heme biosynthetic process / response to light stimulus / Mitochondrial protein degradation / cellular response to dexamethasone stimulus / cholesterol metabolic process / erythrocyte differentiation / generation of precursor metabolites and energy / response to lead ion / ferrous iron binding / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / heme binding / protein homodimerization activity / mitochondrion / identical protein binding
Similarity search - Function
Ferrochelatase / Ferrochelatase, active site / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / Ferrochelatase signature. / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLIC ACID / FE2/S2 (INORGANIC) CLUSTER / Ferrochelatase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.35 Å
AuthorsDailey, H.A. / Wu, C.-K. / Horanyi, P. / Medlock, A.E. / Najahi-Missaoui, W. / Burden, A.E. / Dailey, T.A. / Rose, J.P.
Citation
Journal: Biochemistry / Year: 2007
Title: Altered orientation of active site residues in variants of human ferrochelatase. Evidence for a hydrogen bond network involved in catalysis
Authors: Dailey, H.A. / Wu, C.-K. / Horanyi, P. / Medlock, A.E. / Najahi-Missaoui, W. / Burden, A.E. / Dailey, T.A. / Rose, J.P.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: The 2.0 A Structure of Human Ferrochelatase, the Terminal Enzyme of Heme Biosynthesis
Authors: Wu, C.K. / Dailey, H.A. / Rose, J.P. / Burden, A. / Sellers, V.M. / Wang, B.-C.
#2: Journal: Biochim.Biophys.Acta / Year: 1999
Title: Human Ferrochelatase: Crystallization, Characterization of the [2Fe-2S] Cluster and Determination that the Enzyme is a Homodimer
Authors: Burden, A.E. / Wu, C.-K. / Dailey, T.A. / Busch, J.L.H. / Dhawan, I.K. / Rose, J.P. / Wang, B.C. / Dailey, H.A.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferrochelatase, mitochondrial
B: Ferrochelatase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,92010
Polymers82,1172
Non-polymers2,8038
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-38 kcal/mol
Surface area27240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.686, 94.052, 113.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 65 - 423 / Label seq-ID: 1 - 359

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Ferrochelatase, mitochondrial / E.C.4.99.1.1 / Protoheme ferro-lyase / Heme synthetase


Mass: 41058.254 Da / Num. of mol.: 2 / Fragment: Mature Protein / Mutation: R115L, F337A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FECH / Plasmid: PHDTF20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P22830, EC: 4.99.1.1
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5
Details: MICROBATCH UNDER OIL (70:30 PARAFFIN/SILICONE OIL MIXTURE) METHO USING 2 microliter DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (64 MG/ML IN 50 MM TRIS MOPS, 0.1M KCL, 1% NA-CHOLATE, ...Details: MICROBATCH UNDER OIL (70:30 PARAFFIN/SILICONE OIL MIXTURE) METHO USING 2 microliter DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (64 MG/ML IN 50 MM TRIS MOPS, 0.1M KCL, 1% NA-CHOLATE, 250 MM IMIDAZOLE, PH 8.1) AND PRECIPITANT SOLUTION (0.2 M SODIUM ACETAT TRI HYDRATE, 0.1 M SODIUM CACODYLATE, PH 6.5 IN 30%W/V POLYETHYL GLYCOL 8000 (HAMPTON CRYSTAL SCREEN I-28, HAMPTON RESEARCH), pH 6.50, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2005 / Details: ROSENBAUM
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2→50 Å / Num. obs: 58933 / % possible obs: 90.1 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.23
Reflection shellResolution: 2→2.07 Å / Redundancy: 10 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.39 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
SERGUIdata collection
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1HRK

1hrk


Resolution: 2.35→43.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.661 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.332 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25332 1944 5 %RANDOM
Rwork0.19168 ---
all0.19473 36722 --
obs0.19473 36722 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.034 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 182 342 6166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225978
X-RAY DIFFRACTIONr_angle_refined_deg1.822.0128163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.825707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65723.828256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3515993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8541538
X-RAY DIFFRACTIONr_chiral_restr0.1080.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024388
X-RAY DIFFRACTIONr_nbd_refined0.2230.22804
X-RAY DIFFRACTIONr_nbtor_refined0.310.24140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2390
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.28
X-RAY DIFFRACTIONr_mcbond_it0.8651.53686
X-RAY DIFFRACTIONr_mcangle_it1.39225782
X-RAY DIFFRACTIONr_scbond_it2.2632603
X-RAY DIFFRACTIONr_scangle_it3.3834.52377
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2811 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.240.5
medium thermal0.82
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 145 -
Rwork0.2 2711 -
obs--97.88 %

+
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