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- PDB-1dlw: X-RAY CRYSTAL STRUCTURE OF TRUNCATED HEMOGLOBIN FROM P.CAUDATUM. -

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Basic information

Entry
Database: PDB / ID: 1dlw
TitleX-RAY CRYSTAL STRUCTURE OF TRUNCATED HEMOGLOBIN FROM P.CAUDATUM.
ComponentsHEMOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / GLOBIN FOLD TRUNCATED HEMOGLOBIN NON VERTEBRATE HEMOGLOBIN / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Truncated hemoglobin, group 1 / Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin trHbN
Similarity search - Component
Biological speciesParamecium caudatum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.54 Å
AuthorsPesce, A. / Couture, M. / Guertin, M. / Dewilde, S. / Moens, L. / Bolognesi, M.
CitationJournal: EMBO J. / Year: 2000
Title: A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.
Authors: Pesce, A. / Couture, M. / Dewilde, S. / Guertin, M. / Yamauchi, K. / Ascenzi, P. / Moens, L. / Bolognesi, M.
History
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5312
Polymers11,9141
Non-polymers6161
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.180, 61.180, 35.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein HEMOGLOBIN


Mass: 11914.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium caudatum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P15160
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRUNCATED HEMOGLOBIN OF 116 AMINO ACID RESIDUES PER CHAIN

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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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: AMMONIUM SULPHATE, SODIUM ACETATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
235 %ammonium sulfate1reservoir
350 mMsodium acetate1reservoir
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. all: 36762 / Num. obs: 36762 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 31
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.106 / % possible all: 93.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 88.2 % / Mean I/σ(I) obs: 7

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Processing

Software
NameClassification
SOLVEphasing
WARPmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
RefinementResolution: 1.54→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: AT THE END OF REFINEMENT, THE ANISOTROPIC REFINEMENT OF B-FACTORS WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3672 -RANDOM
Rwork0.133 ---
all0.133 36762 --
obs0.133 36762 96.4 %-
Refinement stepCycle: LAST / Resolution: 1.54→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms837 0 43 207 1087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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