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- PDB-1jzm: Crystal Structure of Scapharca inaequivalvis HbI, I114M Mutant in... -

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Basic information

Entry
Database: PDB / ID: 1jzm
TitleCrystal Structure of Scapharca inaequivalvis HbI, I114M Mutant in the Absence of ligand.
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 / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / Myoglobin-like, M family globin 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 / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2024
Polymers31,9692
Non-polymers1,2332
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-46 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.820, 44.490, 143.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is the dimer found in the asymmetric unit.

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Components

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


Mass: 15984.356 Da / Num. of mol.: 2 / Mutation: I114M
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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 8.5
Details: Phosphate buffer, pH 8.5, Microbatch, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12961
22961
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEApr 4, 2000Yale mirrors
RIGAKU RAXIS IIC2IMAGE PLATEApr 6, 2000Yale Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Yale MirrorsSINGLE WAVELENGTHMx-ray1
2Yale MirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 22491 / Num. obs: 22491 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.256 / Num. unique all: 1909 / % possible all: 81.7

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4SDH (deoxy wild type HbI)

4sdh


Resolution: 1.9→26.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2037889.96 / 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
Rfree0.201 1773 7.9 %RANDOM
Rwork0.171 ---
all0.187 22491 --
obs0.171 22491 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9183 Å2 / ksol: 0.342299 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--1.23 Å20 Å2
3----1.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 86 151 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it3.612
X-RAY DIFFRACTIONc_scangle_it4.922.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.277 153 8 %
Rwork0.234 1748 -
obs--81.3 %
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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