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- PDB-2veb: High resolution structure of protoglobin from Methanosarcina acet... -

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Basic information

Entry
Database: PDB / ID: 2veb
TitleHigh resolution structure of protoglobin from Methanosarcina acetivorans C2A
ComponentsPROTOGLOBIN
KeywordsTRANSPORT PROTEIN / HEMOPROTEIN STRUCTURE / PROTEIN MATRIX TUNNELS / PROTOGLOBIN / METHANOGENESIS / ARCHAEA PROTEIN
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding
Similarity search - Function
Protoglobin / Globin-sensor domain / Protoglobin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / PHOSPHATE ION / Globin-sensor domain-containing protein
Similarity search - Component
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsNardini, M. / Pesce, A. / Thijs, L. / Saito, J.A. / Dewilde, S. / Alam, M. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Moens, L. / Bolognesi, M.
CitationJournal: Embo Rep. / Year: 2008
Title: Archaeal Protoglobin Structure Indicates New Ligand Diffusion Paths and Modulation of Haem-Reactivity.
Authors: Nardini, M. / Pesce, A. / Thijs, L. / Saito, J.A. / Dewilde, S. / Alam, M. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Moens, L. / Bolognesi, M.
History
DepositionOct 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Advisory / Derived calculations ...Advisory / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9416
Polymers23,0111
Non-polymers9315
Water4,774265
1
A: PROTOGLOBIN
hetero molecules

A: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,88312
Polymers46,0222
Non-polymers1,86110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7790 Å2
ΔGint-93.1 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.059, 49.271, 51.513
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTOGLOBIN


Mass: 23010.863 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA ACETIVORANS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8TLY9

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Non-polymers , 5 types, 270 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 101 TO SER

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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: 2.31 Å3/Da / Density % sol: 46.9 % / Description: NONE
Crystal growpH: 4.2 / Details: 0.4 M MONOBASIC AMMONIUM PHOSPHATE, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.3→51.4 Å / Num. obs: 48188 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.7
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 7.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.3→51.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.246 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2432 5 %RANDOM
Rwork0.16 ---
obs0.161 45754 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.11 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.3→51.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 61 265 1917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221725
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.332.0312364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9255195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9723.79387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64715271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.232159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021348
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.2845
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21168
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.271.5982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80121560
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5633875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3084.5799
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
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.172 187
Rwork0.154 3443

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