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- PDB-5c6e: Joint X-ray/neutron structure of equine cyanomet hemoglobin in R state -

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Basic information

Entry
Database: PDB / ID: 5c6e
TitleJoint X-ray/neutron structure of equine cyanomet hemoglobin in R state
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Equine Hemoglobin / R-State
Function / homology
Function and homology information


hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDajnowicz, S. / Sean, S. / Hanson, B.L. / Fisher, S.Z. / Langan, P. / Kovalevsky, A.Y. / Mueser, T.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM071939-01 United States
National Science Foundation (NSF, United States)446218 United States
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Visualizing the Bohr effect in hemoglobin: neutron structure of equine cyanomethemoglobin in the R state and comparison with human deoxyhemoglobin in the T state.
Authors: Dajnowicz, S. / Seaver, S. / Hanson, B.L. / Fisher, S.Z. / Langan, P. / Kovalevsky, A.Y. / Mueser, T.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4566
Polymers31,1712
Non-polymers1,2854
Water2,216123
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,91112
Polymers62,3414
Non-polymers2,5708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area46020 Å2
ΔGint-119 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.860, 63.160, 54.710
Angle α, β, γ (deg.)90.00, 110.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 15138.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P01958
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 16032.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02062
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 290 K / Method: batch mode / pH: 7.2 / Details: ammonium sulfate,HEPES

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU FR-E11.54
NUCLEAR REACTORLANSCE PCS20.7-6.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATESep 16, 2009Osmic Confocal Multilayer
3HE POSITION SENSITIVE DETECTOR2AREA DETECTORNov 25, 2009SERIES OF COLLIMATORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2neutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.71
361
Reflection

Entry-ID: 5C6E

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.7-30.23583994.63.80.064112.9
2-21.581878080.22.70.24223.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.793.80.2873.9191.1
2-2.111.90.3561.4267.9

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Processing

Software
NameVersionClassificationNB
MOSFLMLAUENORMdata reduction
SCALAdata scaling
CNSnCNS 1.0.0phasing
nCNS1.0.0refinement
Refinement

Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDR Free selection details
1.7-30.2X-RAY DIFFRACTION0.2330.0050.211697339145.188.81
2-21.58NEUTRON DIFFRACTION0.3340.030.30175918780579.62RANDOM
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.220.2
Luzzati d res low-5
Luzzati sigma a0.120.15
Luzzati d res high-1.7
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.450.41
Luzzati d res low-5
Luzzati sigma a0.80.77
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 1.7→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 90 123 2416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg16.3
X-RAY DIFFRACTIONx_torsion_impr_deg42.05
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg16.3
NEUTRON DIFFRACTIONx_torsion_impr_deg42.05
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.7-1.780.2541745.30.2744731X-RAY DIFFRACTION0.01967.2
2-2.090.4136350.4182960NEUTRON DIFFRACTION0.05342.3

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