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- PDB-1nwi: Crystal structure of CO-HbI transformed to an unligated state -

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Basic information

Entry
Database: PDB / ID: 1nwi
TitleCrystal structure of CO-HbI transformed to an unligated state
Componentsglobin I
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 / response to hypoxia / heme binding / identical protein binding / metal ion 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: 2.5 Å
AuthorsKnapp, J.E. / Royer JR., W.E.
Citation
Journal: Biochemistry / Year: 2003
Title: Ligand-linked structural transitions in crystals of a cooperative dimeric hemoglobin.
Authors: Knapp, J.E. / Royer Jr., W.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: High resolution crystallographic analysis of a co-operative dimeric hemoglobin
Authors: Royer JR., W.E.
History
DepositionFeb 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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: globin I
B: globin I
C: globin I
D: globin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3318
Polymers63,8654
Non-polymers2,4664
Water2,666148
1
A: globin I
B: globin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1664
Polymers31,9332
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-45 kcal/mol
Surface area12310 Å2
MethodPISA
2
C: globin I
D: globin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1664
Polymers31,9332
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-46 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.810, 44.210, 87.120
Angle α, β, γ (deg.)90.00, 115.38, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer formed either from the A and B chains or from the C and D chains.

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Components

#1: Protein
globin I


Mass: 15966.319 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Gene: HbI / 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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.18 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 296 K / Method: small tubes / pH: 7.5
Details: Sodium and Potassium phosphate, pH 7.5, SMALL TUBES, temperature 296K
Crystal grow
*PLUS
Method: unknown
Details: Summerford, C.M., (1995) Protein Eng., 8, 593., Royer, W.E.,Jr. (1994) J. Mol. Biol., 235, 657.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 29, 2001 / Details: Yale 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: 2.5→40 Å / Num. all: 19646 / Num. obs: 19646 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.239 / Rsym value: 0.239 / % possible all: 85.6
Reflection
*PLUS
Num. measured all: 75147
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 85.5 %

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SDH

3sdh


Resolution: 2.5→30.95 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 949 4.8 %RANDOM
Rwork0.194 ---
all0.197 19623 --
obs0.194 19623 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9588 Å2 / ksol: 0.320278 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20.26 Å2
2---1.59 Å20 Å2
3---1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 172 148 4784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d1.09
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.241 89 4.6 %
Rwork0.235 1845 -
obs-1934 94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM19X.HEMETOPH19X.HEME
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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