[English] 日本語
Yorodumi
- PDB-7sje: Crystal structure of dehaloperoxidase B in complex with p-cymene -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sje
TitleCrystal structure of dehaloperoxidase B in complex with p-cymene
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding
Function / homology
Function and homology information


oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 1-methyl-4-(1-methylethyl)benzene / OXYGEN MOLECULE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / Malewschik, T. / Yun, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: The Multifunctional Globin Dehaloperoxidase as a Biocatalyst in the Oxidation of Monoterpenes
Authors: Malewschick, T. / Yun, D. / de Serrano, V. / Ghiladi, R.A.
History
DepositionOct 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5549
Polymers30,8292
Non-polymers1,7267
Water3,063170
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3575
Polymers15,4141
Non-polymers9434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1974
Polymers15,4141
Non-polymers7833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.472, 66.466, 68.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dehaloperoxidase B


Mass: 15414.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Gold(DE3) / References: UniProt: Q9NAV7

-
Non-polymers , 5 types, 177 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MML / 1-methyl-4-(1-methylethyl)benzene / p-cymene / P-Cymene


Mass: 134.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Sequence detailsLigand MML occupies density that is close to the position of H55 in its alternate conformation. The ...Ligand MML occupies density that is close to the position of H55 in its alternate conformation. The occupancies of the alternate conformations reflect the fact. In the fraction where the ligand is bound, reflected by the occupancy of the ligand, H55 is in the conformation facing outside of the distal side of the heme pocket, with the same occupancy as the bound ligand. When the ligand is not bound, H55 can occupy the inside conformation, also reflected by its occupancy.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2000, ammonium sulfate, Na cacodylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→37.2 Å / Num. obs: 29111 / % possible obs: 98.99 % / Redundancy: 4.8 % / CC1/2: 0.995 / Net I/σ(I): 19.8
Reflection shellResolution: 1.72→1.765 Å / Num. unique obs: 2001 / CC1/2: 0.751

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0267refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.72→37.198 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.997 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2107 1522 5.228 %
Rwork0.1784 27589 -
all0.18 --
obs-29111 98.993 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.838 Å20 Å20 Å2
2---0.367 Å20 Å2
3----0.471 Å2
Refinement stepCycle: LAST / Resolution: 1.72→37.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 118 170 2421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132812
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152516
X-RAY DIFFRACTIONr_angle_refined_deg21.6943891
X-RAY DIFFRACTIONr_angle_other_deg1.5891.6395844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09223.354158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77615492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9731517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023593
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02733
X-RAY DIFFRACTIONr_nbd_refined0.2770.2844
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.22416
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21344
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2152
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.219
X-RAY DIFFRACTIONr_nbd_other0.2150.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.225
X-RAY DIFFRACTIONr_mcbond_it1.0771.4061338
X-RAY DIFFRACTIONr_mcbond_other1.0771.4081339
X-RAY DIFFRACTIONr_mcangle_it1.6642.1131737
X-RAY DIFFRACTIONr_mcangle_other1.6642.1141738
X-RAY DIFFRACTIONr_scbond_it1.5761.6691474
X-RAY DIFFRACTIONr_scbond_other1.5631.6661467
X-RAY DIFFRACTIONr_scangle_it2.482.452131
X-RAY DIFFRACTIONr_scangle_other2.4672.4452120
X-RAY DIFFRACTIONr_lrange_it5.24318.5393590
X-RAY DIFFRACTIONr_lrange_other5.19318.4143563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7650.2941150.252001X-RAY DIFFRACTION99.5765
1.765-1.8130.2431060.2031973X-RAY DIFFRACTION99.4737
1.813-1.8650.2331020.1891916X-RAY DIFFRACTION99.6051
1.865-1.9230.251920.2031875X-RAY DIFFRACTION99.4942
1.923-1.9860.2381110.1891799X-RAY DIFFRACTION99.4792
1.986-2.0550.248860.1761759X-RAY DIFFRACTION99.7297
2.055-2.1330.2221020.1691674X-RAY DIFFRACTION99.4958
2.133-2.220.186860.1611630X-RAY DIFFRACTION99.3056
2.22-2.3180.215830.161559X-RAY DIFFRACTION99.3947
2.318-2.4310.1661030.151476X-RAY DIFFRACTION99.4959
2.431-2.5620.18910.1461424X-RAY DIFFRACTION99.2141
2.562-2.7170.167740.1751354X-RAY DIFFRACTION98.892
2.717-2.9040.234630.1721265X-RAY DIFFRACTION99.3269
2.904-3.1350.227730.1871189X-RAY DIFFRACTION98.4399
3.135-3.4330.208510.1851108X-RAY DIFFRACTION98.8065
3.433-3.8360.215600.166989X-RAY DIFFRACTION97.8545
3.836-4.4250.142530.154875X-RAY DIFFRACTION97.5815
4.425-5.4070.238330.179754X-RAY DIFFRACTION96.4461
5.407-7.5980.26240.229608X-RAY DIFFRACTION96.1948
7.598-37.1980.286140.241351X-RAY DIFFRACTION91.7085
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)
10.27770.30380.13751.3813-0.52550.5043-0.0283-0.00680.0339-0.1758-0.0438-0.04140.07730.02520.07210.03720.02050.01130.01580.00680.01165.6409-2.367221.3788
20.3712-0.0310.01080.2039-0.22240.7449-0.01960.01280.0070.0475-0.00030.0042-0.0538-0.030.01990.03240.0117-0.00070.0096-0.00170.0017-21.3725-4.692719.2391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 137
2X-RAY DIFFRACTION2ALLB1 - 137

+
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