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- PDB-4mwa: 1.85 Angstrom Crystal Structure of GCPE Protein from Bacillus ant... -

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Basic information

Entry
Database: PDB / ID: 4mwa
Title1.85 Angstrom Crystal Structure of GCPE Protein from Bacillus anthracis
Components(4-hydroxy-3-methylbut-2-en-1-yl diphosphate ...) x 5
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / GCPE protein / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Function / homology
Function and homology information


(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (flavodoxin) / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) / 4-hydroxy-3-methylbut-2-enyl-diphosphate synthase activity (flavodoxin) / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial / GcpE TIM-barrel domain / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsMinasov, G. / Wawrzak, Z. / Brunzelle, J.S. / Xu, X. / Cui, H. / Maltseva, N. / Bishop, B. / Kwon, K. / Savchenko, A. / Joachimiak, A. ...Minasov, G. / Wawrzak, Z. / Brunzelle, J.S. / Xu, X. / Cui, H. / Maltseva, N. / Bishop, B. / Kwon, K. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.85 Angstrom Crystal Structure of GCPE Protein from Bacillus anthracis.
Authors: Minasov, G. / Wawrzak, Z. / Brunzelle, J.S. / Xu, X. / Cui, H. / Maltseva, N. / Bishop, B. / Kwon, K. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of ...Authors: Minasov, G. / Wawrzak, Z. / Brunzelle, J.S. / Xu, X. / Cui, H. / Maltseva, N. / Bishop, B. / Kwon, K. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
B: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
C: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
D: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
E: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
F: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
G: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
H: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,76729
Polymers240,2358
Non-polymers1,53221
Water21,0421168
1
A: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
B: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
C: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
D: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,92816
Polymers120,1394
Non-polymers78912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-154 kcal/mol
Surface area39640 Å2
MethodPISA
2
E: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
F: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
G: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
H: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,83913
Polymers120,0964
Non-polymers7439
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-163 kcal/mol
Surface area39230 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18270 Å2
ΔGint-336 kcal/mol
Surface area77330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.676, 162.676, 76.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11B-403-

CL

21D-402-

SO4

31D-402-

SO4

41B-615-

HOH

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Components

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4-hydroxy-3-methylbut-2-en-1-yl diphosphate ... , 5 types, 8 molecules AGBCDFHE

#1: Protein 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase


Mass: 30034.727 Da / Num. of mol.: 2 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS4180, BA_4502, GBAA_4502, gcpE, ispG / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81LV7, EC: 1.17.7.1
#2: Protein 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase


Mass: 30034.727 Da / Num. of mol.: 1 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS4180, BA_4502, GBAA_4502, gcpE, ispG / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81LV7, EC: 1.17.7.1
#3: Protein 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase


Mass: 30077.730 Da / Num. of mol.: 1 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS4180, BA_4502, GBAA_4502, gcpE, ispG / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81LV7, EC: 1.17.7.1
#4: Protein 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase


Mass: 29991.727 Da / Num. of mol.: 3 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS4180, BA_4502, GBAA_4502, gcpE, ispG / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81LV7, EC: 1.17.7.1
#5: Protein 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase


Mass: 30077.727 Da / Num. of mol.: 1 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS4180, BA_4502, GBAA_4502, gcpE, ispG / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81LV7, EC: 1.17.7.1

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Non-polymers , 3 types, 1189 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsPAPAIN WAS ADDED TO CRYSTALLIZATION DROPS, WHICH CAUSED THE CLEAVAGE AFTER THE RESIDUE ARG-273

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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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 0.2M Ammonium sulpfate, 0.1M Bis-tris pH 6.5, 25% (v/v) PEG3350 + 1/10 (v/v) papain; Cryo: paratone, VAPOR DIFFUSION, ...Details: Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 0.2M Ammonium sulpfate, 0.1M Bis-tris pH 6.5, 25% (v/v) PEG3350 + 1/10 (v/v) papain; Cryo: paratone, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2008 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.241
11-K, -H, -L20.26
11-h,-k,l30.268
11K, H, -L40.232
ReflectionResolution: 1.85→30 Å / Num. all: 192231 / Num. obs: 192231 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 35.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.4 / Num. unique all: 9098 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0046refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.77 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.926 / SU ML: 0.067
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16856 9583 5 %RANDOM
Rwork0.12528 ---
all0.12741 182492 --
obs0.12741 182492 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.752 Å2
Baniso -1Baniso -2Baniso -3
1--5.86 Å2-0 Å2-0 Å2
2---5.86 Å2-0 Å2
3---11.72 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15709 0 73 1168 16950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01916213
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216266
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.98121944
X-RAY DIFFRACTIONr_angle_other_deg0.803337369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.30752101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90724.086673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.672152815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.45315122
X-RAY DIFFRACTIONr_chiral_restr0.0850.22602
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0218304
X-RAY DIFFRACTIONr_gen_planes_other0.0170.023442
X-RAY DIFFRACTIONr_mcbond_it1.0221.5478365
X-RAY DIFFRACTIONr_mcbond_other1.0221.5468364
X-RAY DIFFRACTIONr_mcangle_it1.5382.31410479
X-RAY DIFFRACTIONr_mcangle_other1.5382.31410480
X-RAY DIFFRACTIONr_scbond_it1.2121.7277848
X-RAY DIFFRACTIONr_scbond_other1.1861.7177797
X-RAY DIFFRACTIONr_scangle_other1.8052.51811388
X-RAY DIFFRACTIONr_long_range_B_refined4.07513.18219473
X-RAY DIFFRACTIONr_long_range_B_other3.89912.98119101
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 695 -
Rwork0.173 12837 -
obs-12837 94.89 %
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)
10.89660.1436-0.02550.6165-0.04940.51820.0218-0.08990.0940.05750.0044-0.05710.00010.1193-0.02620.03-0.007-0.00540.0893-0.01940.020355.591541.888637.8744
20.78150.11540.00740.33940.06870.70710.0255-0.0632-0.06420.0299-0.0059-0.02320.07210.0429-0.01960.04590.0082-0.00490.03150.00390.006248.66429.724838.5457
30.74090.3775-0.04120.74040.5061.00320.0156-0.00740.04-0.06170.01210.0367-0.0330.1965-0.02770.03390.02380.00620.075-0.00830.011565.606832.927911.6448
40.75430.32460.19080.34590.09510.3778-0.02350.1304-0.1021-0.04270.0191-0.03170.00430.06980.00440.03690.02680.00660.0548-0.01270.017859.685629.7498-0.4513
50.4031-0.0322-0.01060.78290.19420.5355-0.01130.07320.0445-0.06140.05420.15650.0752-0.0594-0.04290.078-0.0225-0.02480.07490.02430.05315.450922.5443-0.001
60.6740.21330.13130.473-0.00850.61960.00360.0433-0.075-0.02510.0310.00910.1033-0.0032-0.03460.05840.001-0.00840.0383-0.00790.012329.582617.34810.1809
71.00660.11680.5680.6769-0.33551.125-0.0112-0.008-0.05510.00030.05260.04610.125-0.1161-0.04140.076-0.00410.00670.02160.00580.018419.64035.77626.5299
80.77050.41440.03120.80580.08720.56360.029-0.0481-0.04690.109-0.0413-0.04890.0962-0.0630.01230.06450.00210.00060.0180.00370.004827.104511.605838.4229
90.71420.1373-0.00870.4070.00410.33630.0183-0.0704-0.11830.0267-0.00140.01150.0241-0.0197-0.01690.0448-0.0028-0.00090.05430.01030.02413.72642.335938.5987
100.89850.2091-0.04160.4285-0.04490.43260.0535-0.01780.06770.01850.00390.0239-0.0568-0.0282-0.05740.05350.00620.00590.0436-0.00170.01297.747557.850237.3163
110.5176-0.04740.30250.4575-0.34740.78070.0507-0.0011-0.0467-0.0015-0.02020.04670.0185-0.1027-0.03060.02480.0157-0.00550.0642-0.01060.0101-9.398953.617910.4669
120.55430.14330.16670.25150.02690.4010.00390.06860.0136-0.0332-0.018-0.026-0.0148-0.04770.01410.04970.02050.00480.08020.01430.00631.106757.4071-0.1613
130.41820.14560.13780.78-0.08830.3826-0.01420.0576-0.0859-0.05750.0421-0.1341-0.02810.0219-0.02790.05240.00340.01510.0708-0.01140.03442.929164.16470.0595
140.67220.3108-0.11950.5403-0.07820.52810.0110.02920.0580.00260.01340.0334-0.0473-0.0117-0.02440.05070.0001-0.00180.04970.00130.005928.792869.39740.2909
150.2563-0.0522-0.09170.62090.19520.36270.01550.02290.00670.01960.0073-0.0644-0.07420.0254-0.02280.0702-0.0048-0.00870.0331-0.00150.007839.632982.191527.674
160.45690.13120.01970.2134-0.07330.37710.0211-0.0270.00760.0783-0.03030.0165-0.02240.03510.00910.0922-0.00250.00430.0426-0.00950.003931.055773.665539.2797
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 150
2X-RAY DIFFRACTION2A151 - 261
3X-RAY DIFFRACTION3B2 - 111
4X-RAY DIFFRACTION4B112 - 260
5X-RAY DIFFRACTION5C3 - 123
6X-RAY DIFFRACTION6C124 - 260
7X-RAY DIFFRACTION7D2 - 123
8X-RAY DIFFRACTION8D124 - 260
9X-RAY DIFFRACTION9E2 - 135
10X-RAY DIFFRACTION10E136 - 261
11X-RAY DIFFRACTION11F2 - 125
12X-RAY DIFFRACTION12F126 - 263
13X-RAY DIFFRACTION13G3 - 123
14X-RAY DIFFRACTION14G124 - 260
15X-RAY DIFFRACTION15H3 - 132
16X-RAY DIFFRACTION16H133 - 257

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