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- PDB-4rc1: Structure of the methanofuran/methanopterin biosynthetic enzyme M... -

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Basic information

Entry
Database: PDB / ID: 4rc1
TitleStructure of the methanofuran/methanopterin biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii with PRPP
ComponentsUPF0264 protein MJ1099
KeywordsUNKNOWN FUNCTION / methanopterin / dihydromethanopterin reductase / flavin / protein cage
Function / homology(5-formylfuran-3-yl)methyl phosphate synthase / (5-formylfuran-3-yl)methyl phosphate synthase / (5-formylfuran-3-yl)methyl phosphate synthase, archaea / 4-HFC-P synthase / methanofuran biosynthetic process / carbon-carbon lyase activity / Ribulose-phosphate binding barrel / PHOSPHATE ION / (5-formylfuran-3-yl)methyl phosphate synthase
Function and homology information
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBobik, T.A. / Morales, E.J. / Cascio, D. / Sawaya, M.R. / Yeates, T.O. / Rasche, M.E.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii.
Authors: Bobik, T.A. / Morales, E.J. / Shin, A. / Cascio, D. / Sawaya, M.R. / Arbing, M. / Yeates, T.O. / Rasche, M.E.
History
DepositionSep 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: UPF0264 protein MJ1099
B: UPF0264 protein MJ1099
C: UPF0264 protein MJ1099
D: UPF0264 protein MJ1099
E: UPF0264 protein MJ1099
F: UPF0264 protein MJ1099
G: UPF0264 protein MJ1099
H: UPF0264 protein MJ1099
I: UPF0264 protein MJ1099
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,40015
Polymers234,8309
Non-polymers5706
Water2,702150
1
A: UPF0264 protein MJ1099
C: UPF0264 protein MJ1099
D: UPF0264 protein MJ1099
hetero molecules

A: UPF0264 protein MJ1099
C: UPF0264 protein MJ1099
D: UPF0264 protein MJ1099
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,93310
Polymers156,5546
Non-polymers3804
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12090 Å2
ΔGint-99 kcal/mol
Surface area49720 Å2
MethodPISA
2
B: UPF0264 protein MJ1099
E: UPF0264 protein MJ1099
F: UPF0264 protein MJ1099
G: UPF0264 protein MJ1099
H: UPF0264 protein MJ1099
I: UPF0264 protein MJ1099
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,93310
Polymers156,5546
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-100 kcal/mol
Surface area49350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.870, 153.030, 132.840
Angle α, β, γ (deg.)90.000, 111.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
UPF0264 protein MJ1099


Mass: 26092.266 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1099 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58499
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0M (NH4)2 SO4, 20 mM Tris HCl pH 8, 100 mM NaCl, 5% glycerol and 4 mM DTT, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0393 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0393 Å / Relative weight: 1
ReflectionResolution: 2.4→65 Å / Num. obs: 102609 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 77.96 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.025 / Net I/σ(I): 9.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.4-2.470.5882.07257477412196.5
2.47-2.530.4642.57268277449199.1
2.53-2.610.3982.96257927194199.2
2.61-2.690.3363.4250537034199.1
2.69-2.780.2474.34240916826198.6
2.78-2.870.1825.49225766554199.2
2.87-2.980.1436.32199366234197.4
2.98-3.10.1257.91213806111198.8
3.1-3.240.1059.7213915865199.2
3.24-3.40.0911.13203595632199
3.4-3.580.07713.14188895308199
3.58-3.80.0714.56173915015198.4
3.8-4.060.06515.35159024707197.9
4.06-4.390.06115.72132344259194.7
4.39-4.810.06217.53140234033198.3
4.81-5.370.06117.98129913670199
5.37-6.210.06217.48114733279199.1
6.21-7.60.05818.1394062754198.8
7.6-10.750.05618.6568352070195.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4U9P

4u9p


Resolution: 2.4→65 Å / Cor.coef. Fo:Fc: 0.9556 / Cor.coef. Fo:Fc free: 0.9412 / SU R Cruickshank DPI: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 5118 4.99 %RANDOM
Rwork0.1929 ---
obs0.1938 102608 98.06 %-
Displacement parametersBiso max: 232.69 Å2 / Biso mean: 103.36 Å2 / Biso min: 39.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.3409 Å20 Å22.569 Å2
2---5.818 Å20 Å2
3---3.4771 Å2
Refine analyzeLuzzati coordinate error obs: 0.518 Å
Refinement stepCycle: LAST / Resolution: 2.4→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16051 0 30 150 16231
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5853SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes391HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2355HARMONIC5
X-RAY DIFFRACTIONt_it16315HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2192SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18870SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16315HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg22054HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion18.27
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2824 341 4.87 %
Rwork0.2336 6661 -
all0.2358 7002 -
obs--98.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.11640.3939-1.69492.0543-0.1672.3733-0.0836-0.134-0.20630.3075-0.04120.0216-0.01050.01180.1248-0.05230.0685-0.0133-0.10060.0661-0.0709-20.345-40.499524.0623
21.65630.1575-0.19272.3129-1.22132.11160.0899-0.0671-0.05790.5569-0.17550.17170.0838-0.18510.08560.2348-0.07030.1371-0.1868-0.0379-0.0961-39.9771-53.289954.6939
33.45070.2624-1.80192.2039-0.39282.32620.44980.73290.8165-0.2630.25750.3727-0.666-0.7184-0.7073-0.03640.20740.1247-0.15680.2985-0.0773-16.8253-13.5835-3.9182
43.4188-0.3517-1.63122.28470.54272.1622-0.60780.8041-0.89-0.27840.01240.40730.5698-0.65420.5954-0.0599-0.22840.1586-0.1915-0.2464-0.0302-19.2852-63.6308-3.1808
52.0830.39260.18972.844-0.71612.55610.2790.06090.77920.95170.08930.5505-0.8777-0.519-0.36830.32950.29210.4333-0.3590.07840.1707-46.9521-16.348344.8875
62.48440.0222-0.02451.7335-0.35742.28620.10230.83110.22850.04530.14570.5213-0.2444-0.8384-0.248-0.40140.20820.03620.26450.29640.0626-55.4394-28.981313.6291
73.81240.0342-0.44141.4255-0.72133.2834-0.2198-0.2161-0.12970.62080.4620.5181-0.5085-1.1484-0.24220.09920.1230.4640.21580.1530.0124-72.8062-52.117668.1585
87.4883-0.8817-0.12033.2782-0.45112.1810.0069-0.04010.23240.15350.03560.9237-0.2369-1.1843-0.0425-0.78720.24240.14040.60790.2115-0.2025-91.8876-30.151127.4252
91.86910.6875-0.32782.8975-1.67122.54930.1975-0.0791-0.5214-0.33640.59941.0380.974-1.2057-0.7969-0.6485-0.39560.02960.36430.16820.166-85.2631-63.725933.1178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-5 - 235
2X-RAY DIFFRACTION2{ B|* }B-6 - 235
3X-RAY DIFFRACTION3{ C|* }C0 - 235
4X-RAY DIFFRACTION4{ D|* }D-6 - 235
5X-RAY DIFFRACTION5{ E|* }E0 - 235
6X-RAY DIFFRACTION6{ F|* }F-2 - 235
7X-RAY DIFFRACTION7{ G|* }G0 - 235
8X-RAY DIFFRACTION8{ H|* }H0 - 235
9X-RAY DIFFRACTION9{ I|* }I0 - 235

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