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- PDB-2bkm: Crystal structure of the truncated hemoglobin from Geobacillus st... -

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Basic information

Entry
Database: PDB / ID: 2bkm
TitleCrystal structure of the truncated hemoglobin from Geobacillus stearothermophilus
ComponentsTRUNCATED HEMOGLOBIN FROM GEOBACILLUS STEAROTHERMOPHILUS
KeywordsOXYGEN STORAGE / HYPOTHETICAL PROTEIN / OXYGEN TRANSPORT / TRANSPORT
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding
Similarity search - Function
Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hypothetical conserved protein
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsIlari, A. / Kjelgaard, P. / von Wachenfeldt, C. / Boffi, A. / Chiancone, E.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Crystal Structure and Ligand Binding Properties of the Truncated Hemoglobin from Geobacillus Stearothermophilus
Authors: Ilari, A. / Kjelgaard, P. / von Wachenfeldt, C. / Catacchio, B. / Chiancone, E. / Boffi, A.
History
DepositionFeb 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Dec 20, 2017Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author / entity_src_gen
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRUNCATED HEMOGLOBIN FROM GEOBACILLUS STEAROTHERMOPHILUS
B: TRUNCATED HEMOGLOBIN FROM GEOBACILLUS STEAROTHERMOPHILUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9458
Polymers29,5302
Non-polymers1,4156
Water6,251347
1
A: TRUNCATED HEMOGLOBIN FROM GEOBACILLUS STEAROTHERMOPHILUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4724
Polymers14,7651
Non-polymers7083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TRUNCATED HEMOGLOBIN FROM GEOBACILLUS STEAROTHERMOPHILUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4724
Polymers14,7651
Non-polymers7083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.123, 99.339, 35.252
Angle α, β, γ (deg.)90.00, 105.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 3 - 130 / Label seq-ID: 1 - 128

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.25347, -0.00705, 0.96732), (0.00609, -0.99997, -0.00569), (0.96732, 0.00445, 0.25351)
Vector: -1.80711, 23.84676, 1.35207)

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Components

#1: Protein TRUNCATED HEMOGLOBIN FROM GEOBACILLUS STEAROTHERMOPHILUS


Mass: 14764.802 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Plasmid: PET101/D-TOPO / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q5L1S0
#2: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 1.92 Å3/Da / Density % sol: 35.34 %
Crystal growpH: 5
Details: PEG 5000 MME 20-25 %, ACETATE BUFFER 0.1 M PH 5.2-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 36594 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.02
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UX8

1ux8


Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.141 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1824 5 %RANDOM
Rwork0.167 ---
obs0.168 34771 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.04 Å2
2---0.23 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 98 347 2525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212279
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6342.0663120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8915254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02422.632114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88415357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4441521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021791
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21327
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21539
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1571.51310
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85722080
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.54331086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.944.51036
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1023 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.30.5
medium thermal0.92
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 108
Rwork0.175 2631

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