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- PDB-3chx: Crystal structure of Methylosinus trichosporium OB3b particulate ... -

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Basic information

Entry
Database: PDB / ID: 3chx
TitleCrystal structure of Methylosinus trichosporium OB3b particulate methane monooxygenase (pMMO)
Components
  • 20-residue peptide
  • 26-residue peptide
  • PmoA
  • PmoB
  • PmoCPrime Minister of Canada
KeywordsMEMBRANE PROTEIN / METHANE / BETA BARREL
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Particulate methane monooxygenase subunit c2. Chain: C / Helix hairpin bin / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal ...Particulate methane monooxygenase subunit c2. Chain: C / Helix hairpin bin / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Helix Hairpins / Jelly Rolls / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / PmoA / PmoB / PmoC
Similarity search - Component
Biological speciesMethylosinus trichosporium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å
AuthorsHakemian, A.S.
CitationJournal: Biochemistry / Year: 2008
Title: The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b.
Authors: Hakemian, A.S. / Kondapalli, K.C. / Telser, J. / Hoffman, B.M. / Stemmler, T.L. / Rosenzweig, A.C.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PmoB
B: PmoA
C: PmoC
D: 20-residue peptide
M: 26-residue peptide
E: PmoB
F: PmoA
G: PmoC
H: 20-residue peptide
N: 26-residue peptide
I: PmoB
J: PmoA
K: PmoC
L: 20-residue peptide
O: 26-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,61524
Polymers314,04315
Non-polymers5729
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55700 Å2
ΔGint-583.7 kcal/mol
Surface area92180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.810, 184.070, 203.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain AAAA,CCCC, using strict)
NCS oper:
IDCodeMatrixVector
1given(-0.3077, 0.6681, 0.6774), (0.3198, 0.7432, -0.5877), (-0.8961, 0.0358, -0.4424)-38.1565, 31.0754, 71.0417
2given(-0.3017, 0.3127, -0.9007), (0.6666, 0.7446, 0.0352), (0.6816, -0.5898, -0.4331)42.6907, 0.284, 75.2426

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Components

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Protein , 3 types, 9 molecules AEIBFJCGK

#1: Protein PmoB


Mass: 43181.145 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria) / Gene: pmoB / References: UniProt: Q9KX50
#2: Protein PmoA


Mass: 28524.338 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria) / Gene: pmoA / References: UniProt: Q50541
#3: Protein PmoC / Prime Minister of Canada


Mass: 29024.742 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria) / Gene: pmoC / References: UniProt: Q9KX51

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Protein/peptide , 2 types, 6 molecules DHLMNO

#4: Protein/peptide 20-residue peptide


Mass: 1720.111 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria)
#5: Protein/peptide 26-residue peptide


Mass: 2230.741 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium (bacteria)

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Non-polymers , 1 types, 9 molecules

#6: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu

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Details

Sequence detailsAUTHORS STATE THAT IT WAS NOT POSSIBLE TO ASSIGN PEPTIDES IN CHAINS D,H,L.M,N, AND O TO A ...AUTHORS STATE THAT IT WAS NOT POSSIBLE TO ASSIGN PEPTIDES IN CHAINS D,H,L.M,N, AND O TO A PARTICULAR SEQUENCE OR CHAIN.

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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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M cacodylate, 10% PEG3000, 0.25 M manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 20, 2005
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.9→37.969 Å / Num. obs: 39753 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 7.5
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2 / Num. measured all: 43098 / Num. unique all: 5723 / Rsym value: 0.376 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.7 Å37.94 Å
Translation3.7 Å37.94 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEW

1yew


Resolution: 3.9→38 Å / FOM work R set: 0.623 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.377 3992 10 %random
Rwork0.342 ---
all-39875 --
obs-39694 99.9 %-
Solvent computationBsol: 114.657 Å2
Displacement parametersBiso mean: 141.814 Å2
Baniso -1Baniso -2Baniso -3
1--2.942 Å20 Å20 Å2
2---84.918 Å20 Å2
3---87.86 Å2
Refinement stepCycle: LAST / Resolution: 3.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18936 0 9 0 18945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.864
Refine LS restraints NCSRms: 0 / Type: strict / Weight: 300
LS refinement shellResolution: 3.9→4.04 Å
RfactorNum. reflection% reflection
Rfree0.534 403 -
Rwork0.556 --
obs-3764 96 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param

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