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- PDB-2grz: 5ns Photoproduct of the M37V mutant of Scapharca HbI -

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Basic information

Entry
Database: PDB / ID: 2grz
Title5ns Photoproduct of the M37V mutant of Scapharca HbI
ComponentsGlobin-1
KeywordsOXYGEN STORAGE/TRANSPORT / oxygen transport / allostery / laue / time-resolved crystallography / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKnapp, J.E. / Pahl, R. / Srajer, V. / Royer Jr., W.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin.
Authors: Knapp, J.E. / Pahl, R. / Srajer, V. / Royer Jr., W.E.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Version format compliance
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Oct 20, 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 1.6Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Globin-1
B: Globin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1596
Polymers31,8702
Non-polymers1,2894
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-54 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.040, 43.930, 83.440
Angle α, β, γ (deg.)90.00, 121.95, 90.00
Int Tables number5
Space group name H-MC121
Number of models2
DetailsThe asymmetric unit includes an intact dimer which is the biological assembly.

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Components

#1: Protein Globin-1 / Globin I / HbI / Dimeric hemoglobin


Mass: 15935.239 Da / Num. of mol.: 2 / Mutation: M37V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Gene: HbI / 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.: 241 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 7.5
Details: 57.5% Saturated Phosphate buffer, SMALL TUBES, temperature 298K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.0-1.4
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2004
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.41
ReflectionResolution: 1.6→20 Å / Num. all: 38050 / Num. obs: 28081 / % possible obs: 73.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2
Reflection shellResolution: 1.6→1.67 Å / % possible all: 33.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
Precognitiondata reduction
Epinormdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GRH

2grh


Resolution: 1.6→16.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2143404.42 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: This structure was refined using difference refinement. The structure factors submitted are a weighted Fo(5ns photoproduct) - Fo (no photolysis) synthesis. The A conformer is the initial ...Details: This structure was refined using difference refinement. The structure factors submitted are a weighted Fo(5ns photoproduct) - Fo (no photolysis) synthesis. The A conformer is the initial starting CO-liganded structure (2GRH) and was not refined against the time-resolved crystallographic data. The B conformer was fitted to the time-resolved data with difference refinement. The occupancies were set based on the fraction of CO ligand photolyzed calculated from the integration of the negative electron density surrounding the CO molecule in its bound state.
RfactorNum. reflection% reflectionSelection details
Rfree0.109 1361 4.8 %RANDOM
Rwork0.106 ---
obs0.106 28081 73.8 %-
all-38050 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.002 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.44 Å2
2---0.38 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.6→16.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 90 241 2561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.182 62 5.1 %
Rwork0.195 1160 -
obs--32.3 %
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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