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- PDB-1jzl: Crystal structure of Sapharca inaequivalvis HbI, I114M mutant lig... -

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Basic information

Entry
Database: PDB / ID: 1jzl
TitleCrystal structure of Sapharca inaequivalvis HbI, I114M mutant ligated to carbon monoxide.
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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)33,2586
Polymers31,9692
Non-polymers1,2894
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-54 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.110, 43.970, 83.440
Angle α, β, γ (deg.)90.00, 122.01, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer formed from the A and B subunits of the assemetric 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: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
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

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 PLATEFeb 14, 2000yale mirrors
RIGAKU RAXIS IIC2IMAGE PLATEFeb 16, 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: 1.5→40 Å / Num. all: 46282 / Num. obs: 40783 / % possible obs: 88.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.235 / Num. unique all: 1842 / % possible all: 39.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SDH

3sdh


Resolution: 1.5→28.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1139634.69 / 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
Rfree0.236 4098 10.1 %RANDOM
Rwork0.215 ---
all0.217 40765 --
obs0.215 40765 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.3873 Å2 / ksol: 0.382028 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.09 Å2
2--1.5 Å20 Å2
3----2.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 90 165 2495
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it0.721.5
X-RAY DIFFRACTIONc_mcangle_it1.122
X-RAY DIFFRACTIONc_scbond_it0.132
X-RAY DIFFRACTIONc_scangle_it0.222.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.318 173 9.2 %
Rwork0.291 1716 -
obs-1889 41.2 %
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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