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- PDB-2z8a: Ligand Migration and Binding in The Dimeric Hemoglobin of Scaphar... -

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Basic information

Entry
Database: PDB / ID: 2z8a
TitleLigand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with CO Bound to HEME and in the Presence of 3 Atoms of XE
ComponentsGlobin-1
KeywordsOXYGEN BINDING / OXYGEN TRANSPORT / ALLOSTERY / OXYGEN AFFINITY / Cytoplasm / Heme / Iron / Metal-binding / OXYGEN STORAGE/TRANSPORT
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 / PHOSPHATE ION / XENON / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsKnapp, J.E. / Royer Jr., W.E. / Nienhaus, K. / Palladino, P. / Nienhaus, G.U.
CitationJournal: Biochemistry / Year: 2007
Title: Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca inaequivalvis
Authors: Nienhaus, K. / Knapp, J.E. / Palladino, P. / Royer Jr., W.E. / Nienhaus, G.U.
History
DepositionSep 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.4Nov 1, 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)33,99011
Polymers32,0812
Non-polymers1,9099
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-59 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.660, 43.390, 82.290
Angle α, β, γ (deg.)90.00, 122.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-9352-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 16040.356 Da / Num. of mol.: 2 / Mutation: I1025W/I2025W
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

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Non-polymers , 5 types, 382 molecules

#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: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.11 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 7.5
Details: 1.5-2.5M PHOSPHATE BUFFER, pH 7.50, SMALL TUBES, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.06→46.3 Å / Num. obs: 118984 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 24.1
Reflection shellResolution: 1.06→1.1 Å / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.286 / % possible all: 90.4

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
BIOCARSdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SDH

3sdh


Resolution: 1.06→46.3 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE MODEL WAS REFINED WITH A COMBINATION OF CNS AND SHELX WITH A ROUND OF MANUAL INTERVENTION IN BETWEEN.
RfactorNum. reflection% reflectionSelection details
Rfree0.162 10566 -RANDOM
Rwork0.143 ---
obs0.143 111984 95.3 %-
Refinement stepCycle: LAST / Resolution: 1.06→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 99 373 2768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.014
X-RAY DIFFRACTIONs_from_restr_planes0.0242
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_zero_chiral_vol0.017
X-RAY DIFFRACTIONs_approx_iso_adps0.077
LS refinement shellResolution: 1.06→1.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.163 --
Rfree-555 -
obs-6547 90.4 %

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