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- PDB-1jzk: Crystal Structure of Scapharca inaequivalvis HbI, I114F mutant (deoxy) -

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Basic information

Entry
Database: PDB / ID: 1jzk
TitleCrystal Structure of Scapharca inaequivalvis HbI, I114F mutant (deoxy)
ComponentsGLOBIN I - ARK SHELL
KeywordsOXYGEN STORAGE/TRANSPORT / invertebrate / hemoglobin / allostery / cooperativity / oxygen-binding / oxygen-transport / heme protein / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKnapp, J.E. / Gibson, Q.H. / Cushing, L. / Royer Jr., W.E.
Citation
Journal: Biochemistry / Year: 2001
Title: Restricting the Ligand-Linked Heme Movement in Scapharca Dimeric Hemoglobin Reveals Tight Coupling between Distal and Proximal Contributions to Cooperativity.
Authors: Knapp, J.E. / Gibson, Q.H. / Cushing, L. / Royer Jr., W.E.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Mutation of Residue Phe97 to Leu Disrupts the Central Allosteric Pathway in Scapharca Dimeric Hemoglobin.
Authors: Pardanani, A. / Gibson, Q.H. / Colotti, G. / Royer Jr., W.E.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: High Resolution Crystallographic Analysis of a Co-operative Dimeric Hemoglobin.
Authors: Royer Jr., W.E.
History
DepositionSep 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLOBIN I - ARK SHELL
B: GLOBIN I - ARK SHELL
C: GLOBIN I - ARK SHELL
D: GLOBIN I - ARK SHELL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4678
Polymers64,0014
Non-polymers2,4664
Water4,107228
1
A: GLOBIN I - ARK SHELL
B: GLOBIN I - ARK SHELL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2344
Polymers32,0012
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-47 kcal/mol
Surface area12280 Å2
MethodPISA
2
C: GLOBIN I - ARK SHELL
D: GLOBIN I - ARK SHELL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2344
Polymers32,0012
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-47 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.720, 44.180, 87.230
Angle α, β, γ (deg.)90.00, 115.49, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is either the AB dimer or the CD dimer found in the assemetric unit.

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Components

#1: Protein
GLOBIN I - ARK SHELL / DIMERIC HEMOGLOBIN / HBI


Mass: 16000.335 Da / Num. of mol.: 4 / Mutation: I114F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Plasmid: PCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQL8 / References: UniProt: P02213
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 7.5
Details: 2.1-2.3M Phosphate buffer, pH 7.5, Microbatch, temperature 296K

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 23, 2001 / Details: mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 29156 / Num. obs: 28828 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.173 / % possible all: 81.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4SDH

4sdh


Resolution: 2.2→37.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1409034.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh&Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1410 4.9 %RANDOM
Rwork0.179 ---
all0.1807 28828 --
obs0.179 28818 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.7878 Å2 / ksol: 0.333933 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-2.46 Å2
2--3.99 Å20 Å2
3----2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 172 228 4876
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it2.231.5
X-RAY DIFFRACTIONc_mcangle_it3.462
X-RAY DIFFRACTIONc_scbond_it4.992
X-RAY DIFFRACTIONc_scangle_it7.162.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.248 109 4.7 %
Rwork0.198 2224 -
obs--80.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM19X.HEMETOPH19X.HEME

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