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- PDB-3m0z: Crystal structure of putative aldolase from Klebsiella pneumoniae. -

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Basic information

Entry
Database: PDB / ID: 3m0z
TitleCrystal structure of putative aldolase from Klebsiella pneumoniae.
Componentsputative aldolaseFructose-bisphosphate aldolase
KeywordsLYASE / MCSG / PSI-2 / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology2-dehydro-3-deoxy-phosphogluconate aldolase / KDGP aldolase / catalytic activity / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Putative periplasmic protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsChang, C. / Rakowski, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative aldolase from Klebsiella pneumoniae.
Authors: Chang, C. / Rakowski, E. / Clancy, S. / Joachimiak, A.
History
DepositionMar 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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: putative aldolase
B: putative aldolase
C: putative aldolase
D: putative aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,65210
Polymers107,0544
Non-polymers5986
Water28,8241600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-103 kcal/mol
Surface area34520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.955, 80.073, 80.911
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
putative aldolase / Fructose-bisphosphate aldolase / Putative periplasmic protein


Mass: 26763.428 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: KPN78578_45670, KPN_04640 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A6THF7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1600 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium sulfate, 0.1M Tris-Cl, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 288952 / Num. obs: 284686 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 23.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.12 / % possible all: 87.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.06 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15487 14413 5.1 %RANDOM
Rwork0.12621 ---
obs0.12767 270215 98.47 %-
all-284628 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.143 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.01 Å2
2--0.14 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7983 0 34 1600 9617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228195
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.97811203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.851129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85724.846324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09151409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1871547
X-RAY DIFFRACTIONr_chiral_restr0.0910.21277
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216289
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4931.55358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19428682
X-RAY DIFFRACTIONr_scbond_it3.48332837
X-RAY DIFFRACTIONr_scangle_it5.0224.52515
X-RAY DIFFRACTIONr_rigid_bond_restr1.5938195
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.199→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 955 -
Rwork0.222 17759 -
obs--89.57 %
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)
10.11550.09330.08420.12690.05050.33180.01620.0020.00430.0206-0.00550.0056-0.00970.0224-0.01070.007-0.00580.00030.0112-0.00410.013640.834915.721614.1535
20.11170.14620.04860.52090.36881.00980.0234-0.01160.00890.0337-0.01370.01740.048-0.0454-0.00980.0119-0.0059-0.00070.0058-0.00280.008834.0465.627125.2498
30.2021-0.0299-0.08110.0892-0.0850.23120.01080.01260.0018-0.021-0.0202-0.00050.02040.00860.00940.00640.0063-0.00110.008-0.00510.013741.035514.0954-15.8776
40.6049-0.0912-0.48170.1080.07461.0038-0.01220.0682-0.0214-0.0164-0.01110.02190.0598-0.10540.02330.01320-0.00910.0172-0.00940.012128.414612.7956-26.0452
50.16690.10260.09810.13830.05210.2750.00810.00650.0109-0.018-0.00470.00940.00650.0089-0.00330.00920.0025-0.00430.00150.00060.013468.378931.9748-0.3784
60.76480.10420.33790.2062-0.06340.7497-0.02890.04290.0463-0.04340.0334-0.0155-0.03160.0756-0.00450.0277-0.00860.01460.0173-0.00310.013280.160132.9113-11.3311
70.12460.1288-0.0860.1828-0.06480.46760.0211-0.01450.0060.0305-0.02150.00560.0407-0.01540.00040.0212-0.0135-0.0010.0090.00180.008769.411130.111429.377
80.20410.355-0.24560.8053-0.48311.06450.033-0.0303-0.0110.0746-0.067-0.0171-0.06720.06070.0340.0274-0.01680.00070.01120.00060.001776.475639.612239.883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 163
2X-RAY DIFFRACTION2A164 - 246
3X-RAY DIFFRACTION3B-2 - 163
4X-RAY DIFFRACTION4B164 - 246
5X-RAY DIFFRACTION5C-2 - 163
6X-RAY DIFFRACTION6C164 - 246
7X-RAY DIFFRACTION7D-2 - 163
8X-RAY DIFFRACTION8D164 - 246

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