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- PDB-3h07: Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthas... -

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Basic information

Entry
Database: PDB / ID: 3h07
TitleCrystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Yersinia pestis CO92
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / ribB / 3 / 4-dihydroxy-2-butanone 4-phosphate synthase / biosynthesis of coenzyme / CSGID / Magnesium / Manganese / Metal-binding / Riboflavin biosynthesis / Structural Genomics / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
DHBP synthase / 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNocek, B. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Yersinia pestis CO92
Authors: Nocek, B. / Gu, M. / Kwon, K. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Structure summary / Category: audit_author / software
Revision 1.4Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
B: 3,4-dihydroxy-2-butanone 4-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)47,3182
Polymers47,3182
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-25 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.907, 70.815, 62.297
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase


Mass: 23658.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q8ZI56, 3,4-dihydroxy-2-butanone-4-phosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.86 Å3/Da / Density % sol: 33.88 %
Crystal growTemperature: 302 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium Sulfate, 0.1M Tris pH 8.5, 25% Peg3350, VAPOR DIFFUSION, SITTING DROP, temperature 302K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 17, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→33.64 Å / Num. all: 27680 / Num. obs: 27484 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G57
Resolution: 1.95→33.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.927 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25321 802 3.2 %RANDOM
Rwork0.19893 ---
obs0.2007 24366 99.23 %-
all-25180 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.253 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å2-0.36 Å2
2---0.62 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 0 158 3227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213109
X-RAY DIFFRACTIONr_bond_other_d0.0010.022046
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9694219
X-RAY DIFFRACTIONr_angle_other_deg1.46134999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8065409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10523.881134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38815514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3811528
X-RAY DIFFRACTIONr_chiral_restr0.10.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213515
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02593
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.831.52043
X-RAY DIFFRACTIONr_mcbond_other0.2121.5836
X-RAY DIFFRACTIONr_mcangle_it1.28523275
X-RAY DIFFRACTIONr_scbond_it2.21731066
X-RAY DIFFRACTIONr_scangle_it3.4044.5944
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 72 -
Rwork0.253 1789 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.17773.19732.062210.76.86314.4051-0.08470.23370.1238-1.2835-0.02930.1156-0.832-0.01350.1140.7710.2417-0.01550.31670.08440.220914.782549.802644.5577
24.20031.3147-0.1360.7394-1.51829.75010.1437-0.26750.47570.121-0.1440.0893-0.7758-0.11360.00030.35730.02950.01120.081-0.00180.149219.567350.633652.8185
31.0563-1.124-0.79924.5583.54226.19320.11560.01410.05770.2306-0.09460.1784-0.0728-0.2121-0.0210.192-0.0320.03130.0843-0.00350.14619.761941.637857.2034
42.280.1693-3.66180.160.11186.95190.02810.04540.1705-0.15810.02890.0729-0.34730.0998-0.0570.43490.0780.05840.19990.05750.197325.81440.842136.8689
51.20011.8305-1.24223.9041-2.34261.46730.1189-0.02460.01860.2211-0.03640.1565-0.13630.0303-0.08260.15560.01460.00540.1178-0.01110.136223.666633.77756.4922
62.95832.79381.03732.9360.05533.31350.1457-0.1271-0.02250.2477-0.07130.0241-0.3705-0.2337-0.07430.15740.00810.00010.1329-0.0020.180718.676627.07453.9777
74.17970.32230.8120.0441-0.03732.00930.00150.056-0.07930.02270.06240.0166-0.2279-0.0434-0.06390.09070.0183-0.00390.20860.00120.207726.498328.502249.3879
83.4293-1.2006-0.66446.72830.08272.12760.0672-0.194-0.14310.0363-0.0692-0.5441-0.48990.66540.00190.1215-0.1448-0.02490.2645-0.01050.174643.939631.61953.4796
91.0898-3.0349-1.43069.8521.29287.22670.24680.01640.2271-0.57750.0905-0.4994-0.4451-0.1436-0.33730.233-0.05590.01620.43590.07040.362139.255933.391638.164
102.27270.7128-0.94191.9102-0.81423.1957-0.0229-0.038-0.30790.06360.0094-0.13680.18270.26770.01350.07490.0123-0.02930.1245-0.02350.141233.597121.218356.5041
114.651.0297-0.85622.1303-2.76543.64610.0463-0.27370.30960.0689-0.08920.0063-0.08680.09760.04290.119-0.00750.00920.1587-0.0060.148328.43124.623660.5634
129.5253-3.57920.22625.2964-1.62255.21270.0142-0.45280.16560.5658-0.0224-0.2452-0.07840.17850.00820.1576-0.0415-0.0460.1766-0.01190.090638.614329.519265.9125
130.0296-0.2532-0.15424.32250.18791.4830.0132-0.04530.0025-0.0461-0.0640.03240.03640.4870.05080.066-0.01870.00270.23780.00950.179237.224623.21155.4926
145.4236-1.4913-2.28522.1919-0.51.69130.23-0.02410.3804-0.4312-0.0994-0.17360.07470.1237-0.13050.3232-0.17470.03410.2572-0.02320.190136.122742.56347.0328
152.1933-0.7845-0.75181.97072.22792.62630.1132-0.27870.0825-0.09540.1055-0.1132-0.17410.2194-0.21870.2353-0.08880.03620.2022-0.05620.143829.675740.384456.7322
160.0502-0.23540.24323.40782.06635.7320.0282-0.0062-0.0155-0.3685-0.06970.0828-0.1763-0.10670.04150.0459-0.0012-0.00090.1588-0.00380.171918.662528.81840.0698
172.01091.3442-1.84381.1744-0.20679.8320.0675-0.06570.0456-0.0206-0.04770.0477-0.2028-0.3065-0.01980.12250.0307-0.00950.1557-0.010.155313.739637.953242.695
180.1810.3685-0.8153.146-0.29854.45790.0375-0.0031-0.1234-0.1071-0.5562-0.2585-0.285-0.31210.51870.12050.0347-0.01020.2115-0.01820.210415.647540.209350.1058
195.6037-0.8465-5.87350.12790.88726.15640.56410.32090.5263-0.0776-0.033-0.0805-0.573-0.3346-0.53110.5059-0.10230.04770.08930.02120.231527.157449.502145.8589
2012.9503-1.6602-4.552613.94030.98194.04930.1781-0.00030.8102-0.31520.0301-0.7169-0.48020.372-0.20830.3647-0.09420.02160.2387-0.01450.281130.384554.856350.981
214.04740.6022-0.49431.05792.96769.63250.69060.0123-0.0470.4377-0.331-0.13240.9734-1.1386-0.35960.5162-0.1234-0.01340.20520.10320.244914.8456-4.811647.3878
224.5568-0.5471-0.74849.4333-2.62497.99420.20690.3951-0.52560.7082-0.3260.39530.5271-0.08370.11910.457-0.0178-0.05690.0748-0.03130.192619.7851-5.442240.6672
231.2962-0.16210.48312.08651.41155.01040.1915-0.0284-0.0482-0.2042-0.24230.22720.3089-0.44750.05080.23160.02-0.04210.0807-0.00140.161120.0253.58336.186
240.7465-0.85282.72680.991-3.135510.01080.03440.0199-0.01970.0182-0.0624-0.00660.09320.12980.0280.291-0.0614-0.04410.20420.03220.249725.9074.337656.5509
252.339-2.15131.77392.9416-3.29975.80070.20860.1773-0.1079-0.1239-0.10180.1817-0.02170.2318-0.10690.1342-0.0322-0.02390.1016-0.0230.149723.785211.475536.9468
262.5456-0.9428-2.06972.02064.355810.04570.1078-0.01950.0002-0.1125-0.08150.07250.093-0.3185-0.02630.2168-0.0206-0.05440.14630.03630.171418.696118.182539.4471
274.5766-1.3286-0.71890.39420.34043.0573-0.06930.0792-0.01690.0349-0.00190.02630.31240.14730.07130.08850.02460.01160.1594-0.00450.195127.876316.04443.3833
280.59060.5521-2.26851.1127-1.040110.6751-0.1805-0.1193-0.2006-0.31160.0289-0.5330.43790.74650.15160.19920.12290.09420.3292-0.04260.311243.391710.17135.31
293.7324-0.97110.8424.3227-2.52929.58370.0487-0.1380.15760.24380.0123-0.43820.08060.7062-0.0610.02580.0166-0.01140.2106-0.01660.182145.192516.893745.3244
303.1127-1.53680.63994.5577-1.63912.80520.07270.08350.2115-0.1674-0.003-0.1583-0.03350.3516-0.06970.0366-0.03940.02960.1498-0.0340.146435.710922.815237.8778
319.9424-1.76140.51390.3471-0.525.43910.13170.11240.1422-0.0072-0.0259-0.0254-0.1283-0.0643-0.10590.1329-0.01030.00550.10980.010.141427.314123.502534.7207
325.45520.4377-2.16655.2341.24314.03150.06410.7077-0.2899-0.7209-0.0803-0.00870.1169-0.03560.01630.15950.05150.01030.2336-0.01320.098636.143615.740828.1751
330.01250.0399-0.16532.88530.50272.80110.0292-0.0241-0.01160.1759-0.137-0.0147-0.20950.48930.10780.06430.0042-0.0020.2251-0.00170.181637.83721.9437.4445
344.19750.03732.75624.9937-1.76442.45220.38880.1032-0.4872-0.0257-0.1623-0.24610.27110.1491-0.22640.23730.167-0.04080.2542-0.02170.231938.76282.073145.5661
356.9662-3.39344.13266.31440.61523.96840.22530.0097-0.19670.18840.11-0.14590.39920.1336-0.33530.27720.0871-0.06470.1696-0.05270.214631.29883.340943.6802
361.6422-0.15910.50113.54271.02570.50160.09080.2625-0.11740.13120.0040.03780.11030.1534-0.09480.24940.0946-0.04920.284-0.08350.195729.56555.901935.3431
374.66890.3395-5.76086.85223.51019.371-0.0626-0.2410.01980.30310.0849-0.02980.26150.3394-0.02230.02420.009-0.02950.1696-0.00790.153618.805316.208351.2551
380.64770.14770.02711.2736-0.48810.4357-0.06950.10070.01760.05270.25180.0660.008-0.2321-0.18220.1011-0.0456-0.00750.21670.03130.192416.024410.683354.3148
391.6807-1.1318-1.4991.64322.39243.52930.35120.17090.0190.1018-0.50110.09070.2746-0.7270.150.3705-0.028300.2307-0.0450.21815.81025.284544.47
408.49180.54754.63317.0633-4.12155.30880.29230.1574-0.7211-0.2646-0.1427-0.40090.34510.1987-0.14960.56480.1385-0.11350.04840.00890.233428.5498-7.048444.7954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 12
2X-RAY DIFFRACTION2A13 - 20
3X-RAY DIFFRACTION3A21 - 31
4X-RAY DIFFRACTION4A32 - 40
5X-RAY DIFFRACTION5A41 - 52
6X-RAY DIFFRACTION6A53 - 60
7X-RAY DIFFRACTION7A61 - 69
8X-RAY DIFFRACTION8A70 - 86
9X-RAY DIFFRACTION9A87 - 93
10X-RAY DIFFRACTION10A94 - 111
11X-RAY DIFFRACTION11A112 - 119
12X-RAY DIFFRACTION12A120 - 128
13X-RAY DIFFRACTION13A129 - 140
14X-RAY DIFFRACTION14A141 - 155
15X-RAY DIFFRACTION15A156 - 173
16X-RAY DIFFRACTION16A174 - 183
17X-RAY DIFFRACTION17A184 - 193
18X-RAY DIFFRACTION18A194 - 201
19X-RAY DIFFRACTION19A202 - 207
20X-RAY DIFFRACTION20A208 - 212
21X-RAY DIFFRACTION21B6 - 12
22X-RAY DIFFRACTION22B13 - 20
23X-RAY DIFFRACTION23B21 - 31
24X-RAY DIFFRACTION24B32 - 40
25X-RAY DIFFRACTION25B41 - 52
26X-RAY DIFFRACTION26B53 - 60
27X-RAY DIFFRACTION27B61 - 70
28X-RAY DIFFRACTION28B71 - 77
29X-RAY DIFFRACTION29B78 - 87
30X-RAY DIFFRACTION30B93 - 107
31X-RAY DIFFRACTION31B108 - 117
32X-RAY DIFFRACTION32B118 - 127
33X-RAY DIFFRACTION33B128 - 140
34X-RAY DIFFRACTION34B141 - 150
35X-RAY DIFFRACTION35B151 - 161
36X-RAY DIFFRACTION36B162 - 173
37X-RAY DIFFRACTION37B174 - 178
38X-RAY DIFFRACTION38B179 - 190
39X-RAY DIFFRACTION39B191 - 202
40X-RAY DIFFRACTION40B203 - 211

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