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- PDB-5h8z: Crystal structure of the C49A C353A mutant Fenna-Matthews-Olson P... -

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Basic information

Entry
Database: PDB / ID: 5h8z
TitleCrystal structure of the C49A C353A mutant Fenna-Matthews-Olson Protein from Chlorobaculum Tepidum
ComponentsBacteriochlorophyll a protein
KeywordsELECTRON TRANSPORT / FMO / antenna complex / photosynthesis
Function / homology
Function and homology information


bacteriochlorophyll binding / photosynthesis / metal ion binding
Similarity search - Function
Bacteriochlorophyll-a Protein / Bacteriochlorophyll A / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Clam / Mainly Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll a protein
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLu, X. / Cuneo, M.J. / Myles, D.A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001035 United States
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Perturbation of bacteriochlorophyll molecules in Fenna-Matthews-Olson protein complexes through mutagenesis of cysteine residues.
Authors: Saer, R. / Orf, G.S. / Lu, X. / Zhang, H. / Cuneo, M.J. / Myles, D.A. / Blankenship, R.E.
History
DepositionDec 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 2.0Nov 21, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / entity_src_nat
Item: _atom_site.occupancy / _entity.pdbx_mutation / _entity.src_method
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 2.2Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Bacteriochlorophyll a protein
C: Bacteriochlorophyll a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,88018
Polymers80,2962
Non-polymers14,58416
Water9,728540
1
A: Bacteriochlorophyll a protein
hetero molecules

A: Bacteriochlorophyll a protein
hetero molecules

A: Bacteriochlorophyll a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,32027
Polymers120,4443
Non-polymers21,87624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area45320 Å2
ΔGint-320 kcal/mol
Surface area40640 Å2
MethodPISA
2
C: Bacteriochlorophyll a protein
hetero molecules

C: Bacteriochlorophyll a protein
hetero molecules

C: Bacteriochlorophyll a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,32027
Polymers120,4443
Non-polymers21,87624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area45220 Å2
ΔGint-317 kcal/mol
Surface area40370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.358, 168.358, 168.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-757-

HOH

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Components

#1: Protein Bacteriochlorophyll a protein / BChl a protein / Fenna-Matthews-Olson protein / FMO protein


Mass: 40148.105 Da / Num. of mol.: 2 / Mutation: C49A, 353A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / Gene: fmoA, CT1499 / Production host: Chlorobium tepidum (bacteria) / References: UniProt: Q46393
#2: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: C55H74MgN4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, 20% 2-proponal, sodium citrate, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 75406 / % possible obs: 100 % / Redundancy: 48.1 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 63.9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ENI

3eni


Resolution: 1.8→19.841 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1997 2.65 %RANDOM
Rwork0.1594 ---
obs0.1602 75382 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 1016 540 7046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156952
X-RAY DIFFRACTIONf_angle_d1.5059732
X-RAY DIFFRACTIONf_dihedral_angle_d12.0442412
X-RAY DIFFRACTIONf_chiral_restr0.081965
X-RAY DIFFRACTIONf_plane_restr0.0081262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.84530.22431400.17035159X-RAY DIFFRACTION100
1.8453-1.89520.23391400.16975138X-RAY DIFFRACTION100
1.8952-1.95090.1981410.17555175X-RAY DIFFRACTION100
1.9509-2.01380.19571400.17765146X-RAY DIFFRACTION100
2.0138-2.08570.20161420.1695192X-RAY DIFFRACTION100
2.0857-2.16910.23391410.17065197X-RAY DIFFRACTION100
2.1691-2.26770.22221420.16875189X-RAY DIFFRACTION100
2.2677-2.38710.19481410.16315185X-RAY DIFFRACTION100
2.3871-2.53640.19621430.17165242X-RAY DIFFRACTION100
2.5364-2.73170.20111420.17065221X-RAY DIFFRACTION100
2.7317-3.00580.1811440.16875269X-RAY DIFFRACTION100
3.0058-3.43880.19231440.16185300X-RAY DIFFRACTION100
3.4388-4.32510.15991450.13875359X-RAY DIFFRACTION100
4.3251-19.84240.17371520.14795613X-RAY DIFFRACTION100

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