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- PDB-4k3z: Crystal structure of D-erythrulose 4-phosphate dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 4k3z
TitleCrystal structure of D-erythrulose 4-phosphate dehydrogenase from Brucella melitensis, solved by iodide SAD
ComponentsD-erythrulose 4-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Brucella melitensis / D-erythrulose 4-phosphate dehydrogenase / iodide SAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity
Similarity search - Function
Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-erythrulose 4-phosphate dehydrogenase
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of D-erythrulose 4-phosphate dehydrogenase from Brucella melitensis, solved by iodide SAD
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Clifton, M.C. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-erythrulose 4-phosphate dehydrogenase
B: D-erythrulose 4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0918
Polymers74,6882
Non-polymers4026
Water9,242513
1
A: D-erythrulose 4-phosphate dehydrogenase
hetero molecules

A: D-erythrulose 4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9976
Polymers74,6882
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area5100 Å2
ΔGint-9 kcal/mol
Surface area23350 Å2
MethodPISA
2
B: D-erythrulose 4-phosphate dehydrogenase
hetero molecules

B: D-erythrulose 4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,18510
Polymers74,6882
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area5390 Å2
ΔGint5 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.500, 103.500, 256.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

21B-743-

HOH

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Components

#1: Protein D-erythrulose 4-phosphate dehydrogenase / EryC family protein


Mass: 37344.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / Gene: BAWG_2138, BMEII0428 / Plasmid: BrmeA.18135.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8YCV0, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6654.4
2
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EmeraldBio JCSG screen, a3: 20% PEG 3350, 200mM ammonium citrate; BrmeA.18135.a.A1.PS01411 at 20mg/ml; crystal from tray 235328a3 incubated with 500mM NaI, 20% EG in 2 steps, pH 7.5, VAPOR ...Details: EmeraldBio JCSG screen, a3: 20% PEG 3350, 200mM ammonium citrate; BrmeA.18135.a.A1.PS01411 at 20mg/ml; crystal from tray 235328a3 incubated with 500mM NaI, 20% EG in 2 steps, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
RIGAKU SATURN 944+1CCDJul 6, 2012
RIGAKU SATURN 944+2CCDMar 30, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray1
2RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 1452860 / Rmerge(I) obs: 0.076 / D res high: 2.3 Å / Num. obs: 68952 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.32.36507498.710.281
2.362.42497099.910.26
2.422.49482210010.219
2.492.57467310010.192
2.572.66459299.910.174
2.662.75441010010.152
2.752.85422010010.132
2.852.97410399.910.117
2.973.1390499.910.094
3.13.25377110010.083
3.253.43354410010.07
3.433.64338299.910.062
3.643.89317099.810.057
3.894.2295510010.052
4.24.6271710010.047
4.65.14246010010.045
5.145.94215399.910.045
5.947.27183999.910.042
7.2710.29142099.610.032
ReflectionResolution: 1.95→50 Å / Num. all: 60098 / Num. obs: 59958 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.2 % / Biso Wilson estimate: 22.275 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 24.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-20.2576.651244239121,297.6
2-2.060.1677.541691040191,294.9
2.06-2.120.15310.142267141031,299
2.12-2.180.13813.953156440131,2100
2.18-2.250.1317.594001739251,2100
2.25-2.330.11519.543918437501,2100
2.33-2.420.1120.353838036611,2100
2.42-2.520.09822.73694135461,2100
2.52-2.630.08924.573515233601,299.9
2.63-2.760.08425.783394332561,299.8
2.76-2.910.07827.933197330791,299.8
2.91-3.080.06731.913013729301,299.6
3.08-3.30.06135.162822427651,299.4
3.3-3.560.05439.292592525781,299.2
3.56-3.90.04942.352347723871,298.9
3.9-4.360.04643.382112921631,298.7
4.36-5.030.04644.811886719231,298
5.03-6.170.04641.531645116431,297.3
6.17-8.720.04239.91274913091,296.3
8.72-500.02842.4969337601,290.4

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.3 Å / D res low: 44.59 Å / FOM : 0.331 / FOM acentric: 0.371 / FOM centric: 0.109 / Reflection: 37265 / Reflection acentric: 31621 / Reflection centric: 5599

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.95→44.86 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2186 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8772 / SU B: 6.721 / SU ML: 0.102 / SU R Cruickshank DPI: 0.15 / SU Rfree: 0.1382 / Isotropic thermal model: isotropic TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 3029 5.1 %RANDOM
Rwork0.1927 ---
obs0.1944 56896 99.75 %-
all-60098 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.19 Å2 / Biso mean: 17.7039 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.25 Å20 Å2
2--0.25 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 26 513 5391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195019
X-RAY DIFFRACTIONr_bond_other_d0.0010.024680
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9486822
X-RAY DIFFRACTIONr_angle_other_deg0.814310745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34323.618246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03215798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5511542
X-RAY DIFFRACTIONr_chiral_restr0.0820.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021176
X-RAY DIFFRACTIONr_mcbond_it0.4420.9772471
X-RAY DIFFRACTIONr_mcbond_other0.4410.9762470
X-RAY DIFFRACTIONr_mcangle_it0.7521.463086
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 205 -
Rwork0.206 4028 -
all-4233 -
obs-4333 97.56 %
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)
10.30590.0469-0.1120.5823-0.35720.7311-0.0009-0.0024-0.0428-0.0021-0.02280.00360.0425-0.02290.02370.07450.03280.00620.0318-0.00390.059516.788130.477149.6477
20.22960.0379-0.00261.19050.4830.77310.00720.01210.0152-0.0395-0.01270.0343-0.0347-0.00240.00550.07390.0571-0.00150.04610.00660.051416.002551.721446.4878
30.31780.0827-0.11660.3029-0.1190.71550.0094-0.01210.00530.0069-0.02930.0515-0.0327-0.05680.01990.06460.05920.00340.0622-0.00060.06596.357750.276956.6018
42.4365-1.19740.71780.70870.12483.9149-0.1158-0.27280.01510.06890.0472-0.00010.2963-0.07270.06860.11640.03030.03530.12980.0160.05494.448838.140675.3592
51.5182-0.1125-0.16990.5757-0.15770.2983-0.0645-0.1718-0.0310.06620.05680.05680.0991-0.00240.00770.09140.03130.02040.05150.00270.036114.876928.993963.658
60.2442-0.1363-0.01690.41940.01120.58280.00270.0337-0.0477-0.0270.01090.0878-0.0302-0.0755-0.01360.080.0291-0.00420.03040.00020.077610.901838.340116.3945
72.8810.07320.45050.44860.10440.50760.03640.0075-0.01890.0420.01010.01470.0555-0.0125-0.04660.09340.03610.00360.01670.00360.044821.902935.816619.7213
80.43940.0182-0.1980.4330.15180.5576-0.050.0165-0.0698-0.04740.01530.00410.0548-0.00810.03480.10520.03170.00120.0158-0.00150.06529.870226.964713.0208
93.041-0.93782.36077.0456-0.75424.91650.10260.21560.094-0.6259-0.163-0.4736-0.0476-0.00040.06040.13890.03490.02560.0817-0.01490.048615.786732.4458-7.6626
100.5732-0.46360.10561.50590.09730.39780.01980.1091-0.0891-0.1965-0.03430.10490.0178-0.03920.01450.11340.0089-0.01860.0464-0.03010.045110.846731.9881.9488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION2A79 - 130
3X-RAY DIFFRACTION3A131 - 233
4X-RAY DIFFRACTION4A234 - 267
5X-RAY DIFFRACTION5A268 - 310
6X-RAY DIFFRACTION6B0 - 57
7X-RAY DIFFRACTION7B58 - 91
8X-RAY DIFFRACTION8B92 - 227
9X-RAY DIFFRACTION9B228 - 254
10X-RAY DIFFRACTION10B255 - 310

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