[English] 日本語
Yorodumi
- PDB-4czc: Crystal structure of the siroheme decarboxylase NirDL in co-compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4czc
TitleCrystal structure of the siroheme decarboxylase NirDL in co-complex with iron-uroporphyrin III analogue
ComponentsNIRD-LIKE PROTEIN
KeywordsTRANSCRIPTION / BIFUNCTIONAL ENZYME / TRANSCRIPTIONAL REGULATOR
Function / homology
Function and homology information


siroheme decarboxylase / lyase activity
Similarity search - Function
Arc Repressor Mutant, subunit A - #2890 / Alpha-Beta Plaits - #3460 / Siroheme decarboxylase , AsnC-like ligand binding domain / : / AsnC-like ligand binding domain / Siroheme decarboxylase NirDL-like HTH domain / : / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #2890 / Alpha-Beta Plaits - #3460 / Siroheme decarboxylase , AsnC-like ligand binding domain / : / AsnC-like ligand binding domain / Siroheme decarboxylase NirDL-like HTH domain / : / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Fe(III) Uroporphyrin / Siroheme decarboxylase
Similarity search - Component
Biological speciesHYDROGENOBACTER THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchmelz, S. / Kriegler, T.M. / Haufschildt, K. / Layer, G. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The Crystal Structure of Siroheme Decarboxylase in Complex with Iron-Uroporphyrin III Reveals Two Essential Histidine Residues
Authors: Haufschildt, K. / Schmelz, S. / Kriegler, T.M. / Neumann, A. / Streif, J. / Arai, H. / Heinz, D.W. / Layer, G.
History
DepositionApr 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NIRD-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1582
Polymers40,2731
Non-polymers8851
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.750, 72.600, 51.110
Angle α, β, γ (deg.)90.00, 102.06, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein NIRD-LIKE PROTEIN / NIRDL


Mass: 40273.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HYDROGENOBACTER THERMOPHILUS (bacteria)
Strain: TK-6 / Description: DSM-6534 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3DFS4
#2: Chemical ChemComp-UFE / Fe(III) Uroporphyrin


Mass: 884.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H36FeN4O16
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.48 Å3/Da / Density % sol: 50.34 % / Description: NONE
Crystal growDetails: FOR THE CRYSTALLIZATION OF THE NIRDL-FE-URO III CO-COMPLEX, NIRDL (7 MG/ML) WAS INCUBATED 30 MIN ON ICE WITH 0.5 MM FE-URO III (DISSOLVED IN 50 % DMSO) PRIOR TO CRYSTAL SETUP. PROTEIN-FE-URO ...Details: FOR THE CRYSTALLIZATION OF THE NIRDL-FE-URO III CO-COMPLEX, NIRDL (7 MG/ML) WAS INCUBATED 30 MIN ON ICE WITH 0.5 MM FE-URO III (DISSOLVED IN 50 % DMSO) PRIOR TO CRYSTAL SETUP. PROTEIN-FE-URO III WAS MIXED WITH EQUAL AMOUNTS OF PRECIPITANT SOLUTION (27 % (V/V) MPD, 0.1 M MES, PH 5.5, AND 9.95 MM SPERMIDINE). CRYSTALS WERE CRYO-PROTECTED WITH 25-33 % (V/V) GLYCEROL OR ADDITIONAL 33 % (V/V) MPD PRIOR TO FLASH FREEZING IN LIQUID NITROGEN.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944PLUS / Detector: CCD / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→28.7 Å / Num. obs: 8137 / % possible obs: 97.8 % / Observed criterion σ(I): 2.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.7
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.57 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CH7

4ch7


Resolution: 2.9→28.68 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 47.553 / SU ML: 0.422 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28432 407 5 %RANDOM
Rwork0.22939 ---
obs0.23215 7730 97.78 %-
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: 51.182 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-4.75 Å2
2--2.43 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 0 61 3 2571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192621
X-RAY DIFFRACTIONr_bond_other_d0.0020.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.6572.0153542
X-RAY DIFFRACTIONr_angle_other_deg0.76935882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71323.279122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67815476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7111523
X-RAY DIFFRACTIONr_chiral_restr0.0690.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022869
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02588
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_it3.6934.7481217
X-RAY DIFFRACTIONr_mcbond_other3.6854.7471216
X-RAY DIFFRACTIONr_mcangle_it6.1677.1071516
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3685.4811404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.902→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.568 32 -
Rwork0.408 533 -
obs--92.32 %
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)
14.65311.04560.09182.3882-0.72392.5508-0.29810.82390.1827-0.28160.33060.19020.0606-0.124-0.03250.3073-0.09380.01040.63830.03280.521980.8910.637112.954
20.57861.0196-0.48832.3088-0.25891.5874-0.03350.0411-0.206-0.17930.1863-0.2279-0.16250.2456-0.15280.3295-0.05440.11220.5596-0.0820.6412104.27824.035114.301
38.805-1.37152.54040.7048-0.41242.46930.0180.61490.3505-0.8061-0.18450.3424-0.78380.39370.16651.8006-0.0972-0.67680.34310.07640.605294.94342.565102.889
43.3271-3.04361.23147.86430.55291.1590.33511.007-0.2893-1.68350.0055-0.5205-0.12880.7047-0.34060.6857-0.13280.22890.7243-0.05080.5056107.64729.677105.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 52
2X-RAY DIFFRACTION2A53 - 234
3X-RAY DIFFRACTION3A235 - 293
4X-RAY DIFFRACTION4A294 - 336

+
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