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- PDB-3kmf: Room Temperature Time-of-Flight Neutron Diffraction Study of Deox... -

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Basic information

Entry
Database: PDB / ID: 3kmf
TitleRoom Temperature Time-of-Flight Neutron Diffraction Study of Deoxy Human Normal Adult Hemoglobin
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / hemolgobin / T-state / deoxy / histidine / protonation / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin 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 / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / 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 / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKovalevsky, A.Y. / Morimoto, Y. / Chatake, T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Direct Determination of Protonation States of Histidine Residues in a 2 A Neutron Structure of Deoxy-Human Normal Adult Hemoglobin and Implications for the Bohr Effect.
Authors: Kovalevsky, A.Y. / Chatake, T. / Shibayama, N. / Park, S.Y. / Ishikawa, T. / Mustyakimov, M. / Fisher, Z. / Langan, P. / Morimoto, Y.
History
DepositionNov 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 13, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_radiation / diffrn_source
Item: _atom_site.occupancy / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ..._atom_site.occupancy / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 2.1Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
C: Hemoglobin subunit beta
E: Hemoglobin subunit alpha
G: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5478
Polymers62,0814
Non-polymers2,4664
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.790, 84.450, 54.350
Angle α, β, γ (deg.)90.00, 99.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Hemoglobin beta chain / Beta-globin / LVV-hemorphin-7


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: batch / pH: 6.7
Details: D2O, BATCH, ammonium sulfate, pH 6.7, batch, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: LANSCE / Beamline: PCS / Wavelength: 0.6-7.0
DetectorType: TIME-OF-FLIGHT MULTIWIRE HE3 / Detector: AREA DETECTOR / Date: Nov 25, 2007
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.61
271
ReflectionResolution: 2→53.7 Å / Num. obs: 33302 / % possible obs: 86.7 % / Observed criterion σ(F): 2.25 / Observed criterion σ(I): 1.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.203 / Net I/σ(I): 4.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 1.5 / % possible all: 74.6

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Processing

Software
NameVersionClassification
PCSsoftwaredata collection
nCNSrefinement
d*TREKMODIFIED FOR NEUTRONdata reduction
LAUENORMMODIFIED FOR NEUTRONdata scaling
nCNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DXM

2dxm


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1192 5.1 %RANDOM
Rwork0.25 ---
obs-24574 63.9 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 172 299 4855
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.008
NEUTRON DIFFRACTIONc_angle_deg1.034

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