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- PDB-6b9t: Crystal structure of MPnS with substrate 2-hydroxyethylphosphonat... -

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Basic information

Entry
Database: PDB / ID: 6b9t
TitleCrystal structure of MPnS with substrate 2-hydroxyethylphosphonate (2-HEP) and Fe(II) bound
ComponentsMethylphosphonate synthase
KeywordsOXIDOREDUCTASE / Phosphonate / Methylphosphonate / Iron
Function / homology
Function and homology information


methylphosphonate synthase / organic phosphonate biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
: / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
(2-hydroxyethyl)phosphonic acid / : / FORMIC ACID / Methylphosphonate synthase
Similarity search - Component
Biological speciesNitrosopumilus maritimus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBorn, D.A. / Drennan, C.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR029205-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3P41GM103403-15S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008313-29 United States
CitationJournal: Science / Year: 2017
Title: Structural basis for methylphosphonate biosynthesis.
Authors: Born, D.A. / Ulrich, E.C. / Ju, K.S. / Peck, S.C. / van der Donk, W.A. / Drennan, C.L.
History
DepositionOct 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)418,70231
Polymers416,9158
Non-polymers1,78723
Water17,781987
1
A: Methylphosphonate synthase
B: Methylphosphonate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6948
Polymers104,2292
Non-polymers4666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16270 Å2
ΔGint-78 kcal/mol
Surface area31970 Å2
MethodPISA
2
C: Methylphosphonate synthase
D: Methylphosphonate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6858
Polymers104,2292
Non-polymers4566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16510 Å2
ΔGint-77 kcal/mol
Surface area33000 Å2
MethodPISA
3
E: Methylphosphonate synthase
F: Methylphosphonate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6858
Polymers104,2292
Non-polymers4566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16230 Å2
ΔGint-82 kcal/mol
Surface area31930 Å2
MethodPISA
4
G: Methylphosphonate synthase
H: Methylphosphonate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6387
Polymers104,2292
Non-polymers4105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15850 Å2
ΔGint-85 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.850, 351.250, 76.870
Angle α, β, γ (deg.)90.00, 103.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methylphosphonate synthase


Mass: 52114.340 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus (strain SCM1) (archaea)
Strain: SCM1 / Gene: mpnS, Nmar_0155 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: A9A1T2, methylphosphonate synthase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-2HE / (2-hydroxyethyl)phosphonic acid


Mass: 126.048 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H7O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 220 mM ammonium chloride, 21% (w/v) PEG 3350, 4 mM 2-hydroxyethylphosphonate, soaked in 220 mM ammonium formate, 21% (w/v) PEG 3350, 2 mM iron(II) chloride, 2.5 mM 2-hydroxyethylphosphonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.35→100 Å / Num. obs: 135649 / % possible obs: 89.8 % / Redundancy: 6.9 % / Rpim(I) all: 0.004 / Rrim(I) all: 0.104 / Net I/σ(I): 15.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.099 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.2377 6643 4.9 %
Rwork0.1904 --
obs0.1927 135624 89.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.8 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28307 0 83 987 29377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329032
X-RAY DIFFRACTIONf_angle_d0.62739357
X-RAY DIFFRACTIONf_dihedral_angle_d14.92917330
X-RAY DIFFRACTIONf_chiral_restr0.0444259
X-RAY DIFFRACTIONf_plane_restr0.0055127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37670.35362570.27984700X-RAY DIFFRACTION99
2.3767-2.40470.33182400.27564772X-RAY DIFFRACTION99
2.4047-2.4340.33062400.27444717X-RAY DIFFRACTION99
2.434-2.46480.32932420.27024740X-RAY DIFFRACTION99
2.4648-2.49720.31322290.2574654X-RAY DIFFRACTION98
2.4972-2.53140.31572520.24984662X-RAY DIFFRACTION97
2.5314-2.56760.32072520.24584476X-RAY DIFFRACTION94
2.5676-2.60590.33932390.25214738X-RAY DIFFRACTION99
2.6059-2.64660.3211960.26214028X-RAY DIFFRACTION92
2.69-2.73640.32311710.26123531X-RAY DIFFRACTION92
2.7364-2.78620.28912550.24674705X-RAY DIFFRACTION99
2.7862-2.83970.31582400.2444831X-RAY DIFFRACTION99
2.8397-2.89770.32612430.23984670X-RAY DIFFRACTION99
2.8977-2.96070.28612710.22924799X-RAY DIFFRACTION99
2.9607-3.02960.29182400.23074596X-RAY DIFFRACTION99
3.0296-3.10530.28732630.23084631X-RAY DIFFRACTION97
3.1053-3.18920.28242290.2274618X-RAY DIFFRACTION96
3.1892-3.28310.2642570.22164742X-RAY DIFFRACTION100
3.2831-3.3890.26362610.20394780X-RAY DIFFRACTION100
3.389-3.51010.26351130.19622336X-RAY DIFFRACTION49
3.5101-3.65060.2452420.19844356X-RAY DIFFRACTION97
3.6506-3.81660.23381740.19073161X-RAY DIFFRACTION98
3.8166-4.01780.20681610.17863207X-RAY DIFFRACTION67
4.0178-4.26930.20672100.1634674X-RAY DIFFRACTION97
4.2693-4.59870.17092150.14624795X-RAY DIFFRACTION100
4.5987-5.06090.18782500.14144800X-RAY DIFFRACTION100
5.0609-5.7920.19052170.14684752X-RAY DIFFRACTION99
5.792-7.29270.19332330.14954707X-RAY DIFFRACTION98
7.2927-46.10770.13712510.12864803X-RAY DIFFRACTION99

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