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- PDB-4u9p: Structure of the methanofuran/methanopterin biosynthetic enzyme M... -

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Basic information

Entry
Database: PDB / ID: 4u9p
TitleStructure of the methanofuran/methanopterin biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii
ComponentsUPF0264 protein MJ1099
KeywordsUNKNOWN FUNCTION / methanopterin / methanofuran
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 / (5-formylfuran-3-yl)methyl phosphate synthase
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / Resolution: 1.7 Å
AuthorsBobik, T.A. / Morales, E. / Shin, A. / Cascio, D. / Sawaya, M.R. / Arbing, M. / Rasche, M.E.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1020200 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5P41RR015301-10 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)8 P41 GM103403-10 United States
CitationJournal: Acta Crystallogr.,Sect.F / 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
DepositionAug 6, 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, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.country ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0264 protein MJ1099
B: UPF0264 protein MJ1099
C: UPF0264 protein MJ1099
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3694
Polymers78,2773
Non-polymers921
Water2,198122
1
A: UPF0264 protein MJ1099
B: UPF0264 protein MJ1099
C: UPF0264 protein MJ1099
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)156,7388
Polymers156,5546
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area11520 Å2
ΔGint-67 kcal/mol
Surface area47240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.760, 152.600, 153.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein UPF0264 protein MJ1099


Mass: 26092.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1099 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q58499
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.25 M sodium citrate pH 4.0 and 26% 2-methyl-2,4-pentanediol
PH range: 4

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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: Aug 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0393 Å / Relative weight: 1
ReflectionResolution: 1.7→76.3 Å / Num. obs: 83236 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.08 Å2 / Rmerge F obs: 0.994 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.091 / Χ2: 1.052 / Net I/σ(I): 9.48 / Num. measured all: 533070
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.740.7560.5522.033437312048108200.6689.8
1.74-1.790.8380.442.613843111694115940.52599.1
1.79-1.840.8870.3413.293765911462113280.40798.8
1.84-1.90.9220.2674.143611311062109630.31999.1
1.9-1.960.9360.2244.963354810729105960.26998.8
1.96-2.030.9510.1786.143206010443102950.21598.6
2.03-2.10.9670.1457.934672995299040.17299.5
2.1-2.190.9720.1259.1333245963595580.14999.2
2.19-2.290.9760.11110.1931526924591460.13298.9
2.29-2.40.9790.09711.4629468883487110.11698.6
2.4-2.530.9830.08512.3225696841682340.10397.8
2.53-2.680.9840.08313.6927365800979110.09998.8
2.68-2.870.9840.07615.3726057743073660.0999.1
2.87-3.10.9860.07216.3323880695068910.08599.2
3.1-3.390.9870.06816.9221105638463160.08198.9
3.39-3.790.9880.06216.8417429580456790.07497.8
3.79-4.380.9890.06118.6218083509950670.07199.4
4.38-5.360.9910.05818.6514965431042640.06898.9
5.36-7.580.990.05817.5910494332532620.06998.1
7.58-76.30.990.05819.536901183518270.06899.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
Cootmodel building
XSCALEdata scaling
AutoSolphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→76.3 Å / Cor.coef. Fo:Fc: 0.8941 / Cor.coef. Fo:Fc free: 0.8793 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 4145 4.98 %RANDOM
Rwork0.2017 ---
obs0.2027 83236 99.63 %-
Displacement parametersBiso max: 112.02 Å2 / Biso mean: 31.99 Å2 / Biso min: 16.06 Å2
Baniso -1Baniso -2Baniso -3
1-5.7004 Å20 Å20 Å2
2--10.4314 Å20 Å2
3----16.1318 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: final / Resolution: 1.7→76.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 6 122 5250
Biso mean--45.26 29.19 -
Num. residues----684
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1879SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes755HARMONIC5
X-RAY DIFFRACTIONt_it5227HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion712SEMIHARMONIC5
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_contact6375SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5227HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7071HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion16.07
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2376 307 5.06 %
Rwork0.2461 5763 -
all0.2457 6070 -
obs--99.63 %
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)
10.91690.4111-0.04170.7703-0.00910.8021-0.0913-0.22750.19740.1040.0303-0.0096-0.08140.10290.0610.00650.0785-0.07640.0656-0.0596-0.13991.646141.4569-19.2559
21.8833-0.2492-0.19931.3606-0.03760.4018-0.0341-0.1278-0.2453-0.0539-0.00140.23440.0096-0.15050.0355-0.01920.0623-0.00690.0631-0.0044-0.1593-24.099218.5748-18.3578
30.2654-0.3245-0.24610.97310.19840.7888-0.0468-0.1294-0.02520.21150.1633-0.17640.06040.0557-0.1166-0.06870.0459-0.0418-0.05560.00620.07482.2025-8.8031-21.152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 234
2X-RAY DIFFRACTION2{ B|* }B0 - 234
3X-RAY DIFFRACTION3{ C|* }C0 - 234

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