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- PDB-2b7h: Hemoglobin from Cerdocyon thous, a canidae from Brazil, at 2.2 An... -

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Basic information

Entry
Database: PDB / ID: 2b7h
TitleHemoglobin from Cerdocyon thous, a canidae from Brazil, at 2.2 Angstroms resolution
Components
  • hemoglobin alpha chain
  • hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / hemoglobin / aquomet / Cerdocyon thous / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / 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 / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesDusicyon thous (crab-eating fox)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEsteves, G.F. / Silva, V.C. / Bloch Jr., C. / Medrano, F.J. / Barbosa, J.A.R.G. / Freitas, S.M.
CitationJournal: To be Published
Title: Crystal structure and biophysical characterization of the Cerdocyon thous, a Canidae from Brazil.
Authors: Esteves, G.F. / Silva, V.C. / Bloch Jr., C. / Medrano, F.J. / Barbosa, J.A.R.G. / Freitas, S.M.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hemoglobin alpha chain
B: hemoglobin beta chain
C: hemoglobin alpha chain
D: hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,30010
Polymers62,6414
Non-polymers2,6586
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-143 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.731, 84.237, 130.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe heterotetramer in the asymmetric unit is the biological assembly.

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Components

#1: Protein hemoglobin alpha chain


Mass: 15270.329 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dusicyon thous (crab-eating fox) / References: UniProt: P60523
#2: Protein hemoglobin beta chain


Mass: 16050.394 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dusicyon thous (crab-eating fox) / References: UniProt: P60526
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 16 % polyethyleneglycol (PEG), 0.1 M Hepes Na, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2004
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 30219 / Num. obs: 30219 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 26.907 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 29.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 7 / Num. unique all: 2948 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FHJ

1fhj


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.249 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.218 / Stereochemistry target values: Engh & Huber
Details: Simulated annealing was performed with the CNS software in the first cycle or refinement. Used TLS refinement. Tyr 145 from the B and D molecules presented weak density for an alternate ...Details: Simulated annealing was performed with the CNS software in the first cycle or refinement. Used TLS refinement. Tyr 145 from the B and D molecules presented weak density for an alternate conformation that was not modeled.
RfactorNum. reflection% reflectionSelection details
Rfree0.23266 1530 5.1 %RANDOM
Rwork0.165 ---
all0.1685 30163 --
obs0.1685 28633 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.571 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---0.15 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4395 0 182 443 5020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224716
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.0656468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1324.341182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43115729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2231510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023548
X-RAY DIFFRACTIONr_nbd_refined0.2160.23065
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23314
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2588
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.215
X-RAY DIFFRACTIONr_mcbond_it0.7071.52886
X-RAY DIFFRACTIONr_mcangle_it1.19624576
X-RAY DIFFRACTIONr_scbond_it2.04832061
X-RAY DIFFRACTIONr_scangle_it2.9964.51884
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 108 -
Rwork0.168 2039 -
obs-2039 99.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.08780.03460.08931.26040.21591.4903-0.02420.0197-0.06270.02310.03490.0420.17830.1128-0.0107-0.09760.00920.0074-0.14150.0019-0.1875-14.725-6.8243-4.3671
24.068-0.2974-1.29651.8756-0.15222.25260.0621-0.00770.60780.11590.063-0.05-0.3672-0.2119-0.1251-0.06720.0291-0.0393-0.11020.0067-0.0144-31.65499.3321-0.0934
33.3970.31970.4971.79030.40251.588-0.0199-0.032-0.2864-0.1146-0.0218-0.13750.1674-0.09910.0417-0.1076-0.01770.0376-0.15710.0152-0.1444-27.9532-11.662923.8805
42.77020.1424-1.14261.92850.84942.59420.02950.01230.2906-0.11090.0139-0.0652-0.29530.1211-0.0433-0.116-0.0116-0.0279-0.1212-0.0061-0.1331-11.21525.193625.1298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1411 - 141
2X-RAY DIFFRACTION1AG2001
3X-RAY DIFFRACTION2BB2 - 1452 - 145
4X-RAY DIFFRACTION2BH2001
5X-RAY DIFFRACTION3CC1 - 1411 - 141
6X-RAY DIFFRACTION3CI2001
7X-RAY DIFFRACTION4DD1 - 1451 - 145
8X-RAY DIFFRACTION4DJ2001

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