[English] 日本語
Yorodumi
- PDB-4xs0: Human methemoglobin in complex with the second and third NEAT dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xs0
TitleHuman methemoglobin in complex with the second and third NEAT domains of IsdH(F365Y/A369F/Y642A) from Staphylococcus aureus
Components
  • (Hemoglobin subunit ...) x 2
  • Iron-regulated surface determinant protein H
KeywordsMETAL TRANSPORT / NEAT / HEME/HEMOGLOBIN BINDING / HEMOGLOBIN / OXYGEN TRANSPORT-PROTEIN BINDING COMPLEX / oxygen transport
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / Hemoglobin, pi ...Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / Hemoglobin, pi / YSIRK Gram-positive signal peptide / Hemoglobin, alpha-type / Hemoglobin, beta-type / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsDickson, C.F. / Jacques, D.A. / Guss, J.M. / Gell, D.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native alpha-globin haem pocket.
Authors: Dickson, C.F. / Jacques, D.A. / Clubb, R.T. / Guss, J.M. / Gell, D.A.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4059
Polymers69,9703
Non-polymers1,4356
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-112 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.219, 92.219, 365.116
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

-
Hemoglobin subunit ... , 2 types, 2 molecules AB

#1: Protein Hemoglobin subunit alpha / / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

-
Protein , 1 types, 1 molecules C

#3: Protein Iron-regulated surface determinant protein H / Haptoglobin receptor A / Staphylococcus aureus surface protein I


Mass: 38929.402 Da / Num. of mol.: 1 / Fragment: UNP residues 326-660 / Mutation: F365Y/A369F/Y642A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: isdH, harA, sasI, SAUSA300_1677 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q2FG07

-
Non-polymers , 4 types, 10 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M K/Na tartrate, 0.1 M tri-sodium citrate pH 5.6, 2 M ammonium sulfate. Cryoprotected in 20% glycerol.
PH range: 5.4 - 5.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9658 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 15, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9658 Å / Relative weight: 1
ReflectionResolution: 2.55→33.39 Å / Num. obs: 31237 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.042 / Net I/σ(I): 9.3 / Num. measured all: 298616 / Scaling rejects: 181
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.55-2.669.70.82523608337090.7660.252100
8.83-33.399.50.0522.486879120.9970.01698.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.5 Å33.39 Å
Translation6.5 Å33.39 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimless0.2.7data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IJ2

4ij2


Resolution: 2.55→33.39 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.2675 / WRfactor Rwork: 0.2428 / FOM work R set: 0.7377 / SU B: 33.489 / SU ML: 0.303 / SU R Cruickshank DPI: 0.4685 / SU Rfree: 0.3027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.469 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1581 5.1 %RANDOM
Rwork0.2594 29544 --
obs0.2608 29544 99.72 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 138.74 Å2 / Biso mean: 67.181 Å2 / Biso min: 28.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å20 Å2
3----2.56 Å2
Refinement stepCycle: final / Resolution: 2.55→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 94 4 4869
Biso mean--55 40 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194989
X-RAY DIFFRACTIONr_bond_other_d0.0010.024708
X-RAY DIFFRACTIONr_angle_refined_deg0.7892.0066802
X-RAY DIFFRACTIONr_angle_other_deg0.642310849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7355598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12724.91222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84715824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1691514
X-RAY DIFFRACTIONr_chiral_restr0.0470.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021093
X-RAY DIFFRACTIONr_mcbond_it1.3675.2752407
X-RAY DIFFRACTIONr_mcbond_other1.3685.2742406
X-RAY DIFFRACTIONr_mcangle_it2.328.8933000
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 113 -
Rwork0.364 2127 -
all-2240 -
obs--99.96 %
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)
10.06880.0804-0.26840.292-0.21851.69240.0987-0.03870.0032-0.0126-0.0123-0.0467-0.20650.011-0.08640.37760.00190.01770.4161-0.06440.056217.5201-32.6746-17.362
20.78390.1596-0.1480.48330.00981.5138-0.07480.0685-0.0099-0.1165-0.0003-0.003-0.2139-0.41580.07510.32140.11370.01090.4905-0.01320.0054-0.6333-33.8024-33.2784
33.5021.99290.15541.27260.07310.12490.3277-0.15640.5809-0.0023-0.19640.2996-0.14760.1645-0.13120.5967-0.13230.33810.2978-0.21220.298630.1516-6.2572-17.8785
41.74910.7175-0.34480.358-0.4221.460.0055-0.30580.0362-0.0475-0.1526-0.01040.08410.11810.14710.161-0.0005-0.0190.61240.00710.022930.8155-43.02414.8942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 999
2X-RAY DIFFRACTION2B1 - 999
3X-RAY DIFFRACTION3C326 - 461
4X-RAY DIFFRACTION4C472 - 655

+
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