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- PDB-3m4r: Structure of the N-terminal Class II Aldolase domain of a conserv... -

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Basic information

Entry
Database: PDB / ID: 3m4r
TitleStructure of the N-terminal Class II Aldolase domain of a conserved protein from Thermoplasma acidophilum
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / short chain dehydrogenase / Class II Aldolase / Adducin head domain / carbohydrate metabolism / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / OXIDOREDUCTASE
Function / homology
Function and homology information


L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / metal ion binding
Similarity search - Function
L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the N-terminal Class II Aldolase domain of a conserved protein from Thermoplasma acidophilum
Authors: Cuff, M.E. / Li, H. / Clancy, S. / Joachimiak, A.
History
DepositionMar 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8443
Polymers24,7431
Non-polymers1012
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.136, 46.136, 203.998
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Uncharacterized protein


Mass: 24743.062 Da / Num. of mol.: 1 / Fragment: Aldolase II domain residues 1-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: PRK08324, Ta0481 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: Q9HKW2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris Propane pH 7.0, 3.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97970, 0.97945
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 28, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.979451
ReflectionRedundancy: 10.6 % / Av σ(I) over netI: 55.71 / Number: 190518 / Rmerge(I) obs: 0.074 / Χ2: 2.68 / D res high: 2 Å / D res low: 50 Å / Num. obs: 18049 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.435096.510.07214.198.9
4.315.4399.310.0587.23610.1
3.764.3199.910.0565.12510.3
3.423.7610010.0594.30310.5
3.173.4210010.0693.77810.5
2.993.1710010.0772.91510.5
2.842.9910010.0892.26810.7
2.712.8410010.0981.99310.7
2.612.7110010.1261.61810.7
2.522.6110010.1391.49910.8
2.442.5210010.1461.18810.6
2.372.4499.910.1661.07210.9
2.312.3710010.1841.0510.6
2.252.3110010.230.9610.9
2.22.2510010.2520.91610.7
2.152.210010.3070.910.9
2.112.1599.910.3380.87610.8
2.072.1199.810.4180.80710.8
2.032.0799.810.5230.80210.8
22.0399.810.6220.78110.9
ReflectionResolution: 2→50 Å / Num. all: 18049 / Num. obs: 18049 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.074 / Χ2: 2.679 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 3.8 / Num. unique all: 856 / Χ2: 0.781 / % possible all: 99.8

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.29 / FOM acentric: 0.35 / FOM centric: 0 / Reflection: 17887 / Reflection acentric: 14809 / Reflection centric: 3078
Phasing MAD setR cullis acentric: 1.63 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 14809 / Reflection centric: 3078
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.5-500.920.40.43254
7.14-12.51.150.60.5215152
5-7.141.690.50.3565242
3.85-51.180.30.31065355
3.12-3.851.350.20.21789430
2.63-3.122.060.10.12646532
2.27-2.632.760.103649618
2-2.273.54004848695
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
151.4529-0.775-0.029-0.0436.748
266.7532-0.640.258-0.0834.915
364.6081-0.447-0.062-0.0675.809
454.3163-0.5820.305-0.0184.262
561.0289-0.877-0.045-0.094.785
686.3637-0.7720.239-0.0766.437
755.8065-0.4530.195-0.11.713
877.9969-0.253-0.025-0.1042.254
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.2640.7080863254
7.14-12.50.360.6140367215152
5-7.140.4340.620807565242
3.85-50.4470.595014201065355
3.12-3.850.4480.555022191789430
2.63-3.120.40.481031782646532
2.27-2.630.2520.294042673649618
2-2.270.1270.145055434848695
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 17887
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.9-10068.30.82504
5.44-6.959.70.868502
4.7-5.4463.20.907504
4.25-4.757.10.91502
3.94-4.2562.70.921508
3.69-3.9458.60.915521
3.49-3.6961.50.924521
3.32-3.4964.20.894536
3.18-3.32630.906585
3.05-3.1858.30.889577
2.93-3.0561.10.873623
2.83-2.9359.90.875624
2.74-2.8365.80.87656
2.66-2.7460.20.868687
2.58-2.6666.20.862665
2.51-2.5864.40.856730
2.45-2.5167.60.858714
2.39-2.4569.50.883763
2.33-2.3966.90.88759
2.28-2.3370.60.857779
2.23-2.2870.80.902795
2.18-2.2375.80.903802
2.14-2.1876.80.892844
2.1-2.1478.10.891817
2.06-2.182.40.883908
2-2.06800.7941461

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2→25.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.877 / SU B: 8.923 / SU ML: 0.115 / SU R Cruickshank DPI: 0.163 / SU Rfree: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 913 5.1 %RANDOM
Rwork0.186 ---
all0.188 17900 --
obs0.188 17900 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.66 Å2 / Biso mean: 27.496 Å2 / Biso min: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20.81 Å20 Å2
2--1.63 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2→25.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 2 142 1756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221699
X-RAY DIFFRACTIONr_bond_other_d0.0010.021132
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9592318
X-RAY DIFFRACTIONr_angle_other_deg0.92232781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87124.18974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52715287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8821511
X-RAY DIFFRACTIONr_chiral_restr0.090.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_mcbond_it0.8261.51085
X-RAY DIFFRACTIONr_mcbond_other0.2281.5443
X-RAY DIFFRACTIONr_mcangle_it1.40321760
X-RAY DIFFRACTIONr_scbond_it2.2633614
X-RAY DIFFRACTIONr_scangle_it3.3934.5548
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 66 -
Rwork0.225 1185 -
all-1251 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -9 Å / Origin y: 18.2991 Å / Origin z: 15.1226 Å
111213212223313233
T0.0975 Å20.0373 Å20.0651 Å2-0.17 Å2-0.0632 Å2--0.1845 Å2
L2.9699 °2-0.7486 °2-1.7352 °2-2.2515 °21.8486 °2--5.3349 °2
S0.0041 Å °-0.1185 Å °0.086 Å °0.3052 Å °-0.1755 Å °0.2268 Å °-0.0204 Å °-0.2579 Å °0.1713 Å °

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