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- PDB-2vee: Structure of protoglobin from Methanosarcina acetivorans C2A -

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Basic information

Entry
Database: PDB / ID: 2vee
TitleStructure 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 / Globin-sensor domain-containing protein
Similarity search - Component
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Advisory / Other / Version format compliance
Revision 1.2Dec 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
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.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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTOGLOBIN
B: PROTOGLOBIN
C: PROTOGLOBIN
D: PROTOGLOBIN
E: PROTOGLOBIN
F: PROTOGLOBIN
G: PROTOGLOBIN
H: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,01916
Polymers184,0878
Non-polymers4,9328
Water4,288238
1
A: PROTOGLOBIN
C: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2554
Polymers46,0222
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-23.6 kcal/mol
Surface area19020 Å2
MethodPQS
2
B: PROTOGLOBIN
D: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2554
Polymers46,0222
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-29.9 kcal/mol
Surface area19200 Å2
MethodPQS
3
E: PROTOGLOBIN
F: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2554
Polymers46,0222
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-23.5 kcal/mol
Surface area19140 Å2
MethodPQS
4
G: PROTOGLOBIN
H: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2554
Polymers46,0222
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-28.3 kcal/mol
Surface area18980 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.930, 48.531, 161.072
Angle α, β, γ (deg.)90.00, 98.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 10
2114B1 - 10
3114C1 - 10
4114D1 - 10
5114E1 - 10
6114F1 - 10
7114G1 - 10
8114H1 - 10
1214A20 - 158
2214B20 - 158
3214C20 - 158
4214D20 - 158
5214E20 - 158
6214F20 - 158
7214G20 - 158
8214H20 - 158
1314A165 - 200
2314B165 - 200
3314C165 - 200
4314D165 - 200
5314E165 - 200
6314F165 - 200
7314G165 - 200
8314H165 - 200

NCS oper:
IDCodeMatrixVector
1given(0.99932, 0.03512, -0.01092), (-0.03474, 0.99885, 0.03318), (0.01207, -0.03277, 0.99939)52.09735, -1.08255, 1.75046
2given(-0.99621, -0.08697, 0.00087), (-0.08653, 0.99205, 0.09141), (-0.00882, 0.09099, -0.99581)-59.82299, -4.35538, 38.42772
3given(-0.99825, -0.05874, 0.00639), (-0.05813, 0.99573, 0.07171), (-0.01058, 0.07121, -0.99741)-8.22991, -2.56441, 40.14032
4given(0.99653, 0.04249, 0.07157), (-0.04498, 0.99843, 0.03347), (-0.07003, -0.03657, 0.99687)-6.48634, 21.24092, 37.35857
5given(-0.99661, -0.03803, -0.07289), (-0.04228, 0.99744, 0.05768), (0.07051, 0.06057, -0.99567)-63.39901, 20.8503, 80.23566
6given(-0.99605, -0.07859, -0.04143), (-0.08176, 0.99333, 0.08135), (0.03476, 0.08442, -0.99582)-13.71388, 19.77637, 81.3236
7given(0.99886, 0.00524, 0.04736), (-0.0054, 0.99998, 0.00318), (-0.04735, -0.00343, 0.99887)44.38855, 23.58559, 40.20804

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Components

#1: Protein
PROTOGLOBIN


Mass: 23010.863 Da / Num. of mol.: 8 / 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
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 101 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN G, CYS 101 TO SER ENGINEERED RESIDUE IN CHAIN H, 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: 2.25 Å3/Da / Density % sol: 45.3 % / Description: NONE
Crystal growpH: 7.5
Details: 15% ISOPROPANOL, 20% PEG 400, 0.1 M NA-HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.6→58.4 Å / Num. obs: 47411 / % possible obs: 97.3 % / Observed criterion σ(I): 2.5 / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEB

2veb


Resolution: 2.6→160.13 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 27.049 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2389 5 %RANDOM
Rwork0.205 ---
obs0.208 45011 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20.49 Å2
2---0.53 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→160.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12728 0 344 238 13310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02213640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1642.02218688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36451528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88723.678696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.364152144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8111572
X-RAY DIFFRACTIONr_chiral_restr0.0810.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210736
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.26710
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.29208
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2468
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5681.57818
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.926212384
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.36836893
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2224.56280
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

Ens-ID: 1 / Number: 1526 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.250.5
2Bmedium positional0.280.5
3Cmedium positional0.240.5
4Dmedium positional0.240.5
5Emedium positional0.250.5
6Fmedium positional0.240.5
7Gmedium positional0.230.5
8Hmedium positional0.270.5
1Amedium thermal0.142
2Bmedium thermal0.152
3Cmedium thermal0.142
4Dmedium thermal0.142
5Emedium thermal0.142
6Fmedium thermal0.142
7Gmedium thermal0.142
8Hmedium thermal0.152
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 169
Rwork0.27 3346

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