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- PDB-1nwn: Crystals of CO-HbI in which the structure was converted to its un... -

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Basic information

Entry
Database: PDB / ID: 1nwn
TitleCrystals of CO-HbI in which the structure was converted to its unligated state, and then converted back to its original CO-ligated state.
Componentsglobin I
KeywordsOXYGEN STORAGE/TRANSPORT / Invertebrate / hemoglobin / allostery / cooperative / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: globin I
B: globin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2226
Polymers31,9332
Non-polymers1,2894
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-54 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.620, 43.510, 83.110
Angle α, β, γ (deg.)90.00, 121.88, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe AB dimer is the biological unit

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Components

#1: Protein globin I


Mass: 15966.319 Da / Num. of mol.: 2
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.: 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.: 25 / 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: 2.16 Å3/Da / Density % sol: 42.71 %
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

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATESep 5, 2001Yale mirrors
RIGAKU RAXIS IIC2IMAGE PLATESep 14, 2001Yale 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: 2.8→40 Å / Num. all: 6301 / Num. obs: 6301 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.261 / Num. unique all: 531 / % possible all: 75.9
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 15137
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 74.1 %

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Processing

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

3sdh


Resolution: 2.8→37.79 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 343 5.6 %RANDOM
Rwork0.222 ---
all0.223 6123 --
obs0.222 6123 86.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8126 Å2 / ksol: 0.343163 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å21.76 Å2
2--7.34 Å20 Å2
3----7.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 90 25 2347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d1.41
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.079 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.402 26 4.9 %
Rwork0.319 505 -
obs-531 75.9 %
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: 2.8 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.398 / Rfactor Rwork: 0.32

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