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- PDB-7l2a: Molybdopterin cofactor biosynthesis protein E from Burkholderia m... -

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Basic information

Entry
Database: PDB / ID: 7l2a
TitleMolybdopterin cofactor biosynthesis protein E from Burkholderia multivorans ATCC 17616
ComponentsMPT synthase subunit 2
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / Molybdenum cofactor biosynthesis protein E / moaE / MPT synthase subunit 2 / molybdopterin biosynthesis / Burkholderia multivorans / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologymolybdopterin synthase activity / molybdopterin synthase / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Mo-molybdopterin cofactor biosynthetic process / cytosol / IMIDAZOLE / Molybdopterin synthase catalytic subunit
Function and homology information
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Molybdopterin cofactor biosynthesis protein E from Burkholderia multivorans ATCC 17616
Authors: Calhoun, B. / Weiss, M.J. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Oct 22, 2025Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPT synthase subunit 2
B: MPT synthase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1717
Polymers36,8222
Non-polymers3495
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint2 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.730, 72.660, 105.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 13 or resid 15...
d_2ens_1(chain "B" and ((resid 0 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISLEUA1 - 14
d_12ens_1ALALEUA16 - 21
d_13ens_1ALAALAA23
d_14ens_1ASNALAA25 - 32
d_15ens_1PHEPHEA34
d_16ens_1GLYGLYA36 - 51
d_17ens_1THRTHRA53 - 123
d_18ens_1GLUSERA126 - 133
d_19ens_1ALATRPA138 - 142
d_110ens_1DMSDMSD
d_21ens_1HISLEUE5 - 18
d_22ens_1ALALEUE20 - 25
d_23ens_1ALAALAE27
d_24ens_1ASNALAE29 - 36
d_25ens_1PHEPHEE38
d_26ens_1GLYASNE40 - 46
d_27ens_1ALAGLYE53 - 61
d_28ens_1THRTRPE63 - 146
d_29ens_1DMSDMSG

NCS oper: (Code: givenMatrix: (-0.389527346283, 0.735325382773, 0.554585455947), (0.725574269799, -0.125881548186, 0.676532197927), (0.567283373195, 0.665920728973, -0.484498872259)Vector: 52. ...NCS oper: (Code: given
Matrix: (-0.389527346283, 0.735325382773, 0.554585455947), (0.725574269799, -0.125881548186, 0.676532197927), (0.567283373195, 0.665920728973, -0.484498872259)
Vector: 52.2037117513, -0.12428446416, -57.0929504909)

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Components

#1: Protein MPT synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / ...Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / Molybdopterin-converting factor large subunit / Molybdopterin-converting factor subunit 2


Mass: 18410.807 Da / Num. of mol.: 2 / Fragment: BumuA.00098.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: moaE, BMULJ_01820 / Plasmid: BumuA.00098.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3KFN7, molybdopterin synthase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen, E3: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol, 0.1 M ...Details: Molecular Dimensions Morpheus screen, E3: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol, 0.1 M MES/imidazole pH 6.5: BumuA.00098.a.B1.PS37859 at 41.7mg/ml + 0.5% beta-octyl-glucoside: cryo: direct: tray 317330e3, puck xxu3-3.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 32130 / % possible obs: 99.9 % / Redundancy: 6.821 % / Biso Wilson estimate: 39.047 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.045 / Χ2: 0.942 / Net I/σ(I): 23.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.94.2410.4072.8823190.9460.46599.5
1.9-1.955.1550.3274.0622590.9710.364100
1.95-2.016.5410.2685.822370.9850.291100
2.01-2.077.3360.2127.9621810.9920.228100
2.07-2.147.3590.1659.9520700.9940.177100
2.14-2.217.3550.12613.0420290.9970.135100
2.21-2.297.3410.09815.819600.9970.105100
2.29-2.397.3470.08517.8418890.9980.091100
2.39-2.497.3350.07221.2618200.9990.077100
2.49-2.627.3290.0625.4817360.9990.064100
2.62-2.767.3080.05328.8416520.9990.057100
2.76-2.937.2960.04534.3615760.9990.048100
2.93-3.137.2620.03939.1714950.9990.042100
3.13-3.387.2030.03544.0613820.9990.038100
3.38-3.77.1420.03348.6612880.9990.036100
3.7-4.147.0740.03250.3111780.9990.034100
4.14-4.787.0220.0352.8910410.9990.033100
4.78-5.856.9370.0352.158850.9990.033100
5.85-8.276.6980.02851.667110.9990.031100
8.27-505.780.03249.554220.9980.03598.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QIE as per MoRDa

2qie


Resolution: 1.85→42.76 Å / SU ML: 0.1952 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 2018 6.29 %0
Rwork0.1887 30086 --
obs0.191 32104 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.93 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 21 178 2418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782330
X-RAY DIFFRACTIONf_angle_d0.93933173
X-RAY DIFFRACTIONf_chiral_restr0.0641357
X-RAY DIFFRACTIONf_plane_restr0.0091414
X-RAY DIFFRACTIONf_dihedral_angle_d12.0241822
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.82817564282 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.32211300.29382095X-RAY DIFFRACTION99.29
1.9-1.950.29971270.25732113X-RAY DIFFRACTION99.78
1.95-20.30361350.262139X-RAY DIFFRACTION99.69
2-2.070.29191370.21032153X-RAY DIFFRACTION99.83
2.07-2.140.22421320.18762097X-RAY DIFFRACTION99.91
2.14-2.230.20231120.18062155X-RAY DIFFRACTION99.96
2.23-2.330.21411490.18972124X-RAY DIFFRACTION100
2.33-2.450.24831580.19412120X-RAY DIFFRACTION100
2.45-2.610.21131510.20262132X-RAY DIFFRACTION99.96
2.61-2.810.25261470.19932166X-RAY DIFFRACTION99.91
2.81-3.090.23991540.19812133X-RAY DIFFRACTION100
3.09-3.540.2121520.19032164X-RAY DIFFRACTION100
3.54-4.460.19761540.16652204X-RAY DIFFRACTION100
4.46-42.760.21271800.1732291X-RAY DIFFRACTION99.76
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)
12.789405957941.16310976301-1.642629802861.97356759602-1.223143691067.574558931610.05051322698090.4356877697390.0877479073422-0.223459516535-0.01071061875530.395853910515-0.175431929613-0.768568122416-0.0311316737640.2972338174770.0206060793556-0.05604126695170.310577450437-0.04283672789150.28210769826111.1873582129-4.74662884281-35.4128319747
23.432301332420.582329517292-0.9298795582993.78051537895-0.4609769069224.31615098560.0224525972515-0.164288096184-0.1253499122910.508671351855-0.03907166849440.5160915395780.202041471812-0.314338370001-0.004013951684720.317693529504-0.008938855025080.01281772280060.290618944263-0.05090108295570.2429543058989.37266109156-3.56257663357-20.6443630014
33.125131248341.26801383705-1.69542387753.81226849039-0.9179971955524.24451395609-0.0110081206399-0.0217444981468-0.04319918921770.275532299178-0.02623918394290.145926887057-0.122049451995-0.2458436861570.06120811137130.2910526301930.00751324832166-0.01299058564410.242346062002-0.02319343069660.25210883927114.3393025234-3.58528596673-25.4193038116
46.071402158812.64669569969-2.095382601758.437650917110.4642791510496.53557636446-0.378759136591-0.259822351423-1.450829971660.386804344127-0.402107795099-1.177677060271.71967304959-0.8204594662070.8219597583410.952271155004-0.1279587900570.1952871047490.5597191178370.04526495741380.5535919513185.80332742737-13.3945955639-5.63502592399
53.123589865043.17078337127-3.957537569443.18346502834-3.957608216894.963359700890.264980969939-0.714511207798-0.3985040249781.13929410914-0.286441698517-0.743743746628-0.3799599851730.3628326412450.1921660637660.582360151878-0.0283727751849-0.07832302928420.483608393689-0.008628992225190.40344642260520.28914425954.0260788777-14.5315264336
61.22020651528-1.12615159883-0.2696430058051.493115853470.2489685137260.05677530925710.3531473565730.655901985407-0.220889605327-2.00680285339-0.5008370826931.22534907508-1.28430042819-0.8603768987730.2077109463571.258288233120.2507702634930.08001904130050.6681830109810.02491913363250.69244952515632.2116515796-27.4825186504-42.5532556895
73.569616060680.1622530768510.5228664878455.09232493011-3.705348600873.101385287540.006686148867440.404919836859-0.309767413138-0.5774300396920.01215266040170.03452395885880.6925951321530.096380865989-0.04882915723770.463689007167-0.00375607505517-0.02677835981690.281314323696-0.04380362304770.29366425781923.3891326293-16.0568888936-40.2745761208
80.934052782992-1.254416392061.595339561154.93360015177-3.26542854217.18888949331-0.03144982859070.1878792179710.00914872471862-0.0861764103129-0.08788955462320.0346129739266-0.6029128244960.04592804744320.08747577094940.294852314817-0.0214554816745-0.02466406468490.287561487433-0.006413370334390.26054105859821.8346198129-5.98042420606-42.1886048957
95.91823670533-4.912862429611.789326668724.05025795305-1.239515883614.311974951460.5407341321.451202135650.436389708667-1.1172361486-0.82234313622-1.254026394610.6354428118431.663712176580.2439614777270.6370230061020.1396353155640.2041570028570.7696015340710.1196910159140.60412456022736.1025861422-8.34448853009-52.6771820268
107.20839999437-3.78848501099-0.2418404632716.30366494995-1.274502393132.647635811340.110933913981-0.08921382484920.293254350318-0.103796859335-0.209567613106-0.9626534262030.4951843527322.25173437992-0.06238649670820.2641312284890.0127302166475-0.003369501368510.5101466691370.04991476660980.52075387397239.9284721732-10.883076466-36.6353508727
111.83544553785-0.4533021600660.8870719775263.19995991247-0.6972773077788.31872647470.04978904614980.08080772466680.0948325520987-0.0361152357988-0.0306826737961-0.2265399944150.1684829925930.455811890931-0.009672510255680.199993124817-0.00339712482788-0.02003023990360.241430030762-0.01101816683360.29345196144428.850074872-7.02180848173-36.8570666436
127.515090797580.1141433764950.2235371378722.876365700811.358768347416.505595037290.1218202762161.4256027191.46795194806-1.02017585864-0.177121708387-0.176796574975-0.2012758635941.845986883590.2915785377870.5280420114640.01487199139670.07558597581170.9437700377130.2770941651160.65950630368836.6664884973-1.80753081039-53.6237093687
136.682171491171.171150636450.4492020648883.03088337744-2.128250220376.98658764645-0.2328326121650.6475648724361.078589382390.0354804766354-0.195203022857-0.545902314249-0.7009433085541.838257629360.2963753339860.447164510324-0.01141848182670.04764225146610.6383767330.09654441763490.78883103755438.24159670621.51067464568-42.6188259807
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 36 )AA0 - 361 - 37
22chain 'A' and (resid 37 through 72 )AA37 - 7238 - 67
33chain 'A' and (resid 73 through 127 )AA73 - 12768 - 122
44chain 'A' and (resid 128 through 137 )AA128 - 137123 - 130
55chain 'A' and (resid 138 through 153 )AA138 - 153131 - 146
66chain 'B' and (resid -4 through 3 )BE-4 - 31 - 8
77chain 'B' and (resid 4 through 22 )BE4 - 229 - 27
88chain 'B' and (resid 23 through 48 )BE23 - 4828 - 53
99chain 'B' and (resid 49 through 56 )BE49 - 5654 - 61
1010chain 'B' and (resid 57 through 72 )BE57 - 7262 - 77
1111chain 'B' and (resid 73 through 120 )BE73 - 12078 - 125
1212chain 'B' and (resid 121 through 134 )BE121 - 134126 - 135
1313chain 'B' and (resid 135 through 149 )BE135 - 149136 - 146

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