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- PDB-3ocr: Crystal structure of aldolase II superfamily protein from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 3ocr
TitleCrystal structure of aldolase II superfamily protein from Pseudomonas syringae
ComponentsClass II aldolase/adducin domain protein
KeywordsLYASE / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG
Function / homologyL-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 / 3-Layer(aba) Sandwich / Alpha Beta / Class II aldolase/adducin domain protein
Function and homology information
Biological speciesPseudomonas syringae pv. phaseolicola 1448A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChang, C. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of aldolase II superfamily protein from Pseudomonas syringae
Authors: Chang, C. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class II aldolase/adducin domain protein
B: Class II aldolase/adducin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5743
Polymers59,4782
Non-polymers961
Water6,035335
1
A: Class II aldolase/adducin domain protein

A: Class II aldolase/adducin domain protein

A: Class II aldolase/adducin domain protein

A: Class II aldolase/adducin domain protein


Theoretical massNumber of molelcules
Total (without water)118,9574
Polymers118,9574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area11150 Å2
ΔGint-43 kcal/mol
Surface area37160 Å2
MethodPISA
2
B: Class II aldolase/adducin domain protein
hetero molecules

B: Class II aldolase/adducin domain protein
hetero molecules

B: Class II aldolase/adducin domain protein
hetero molecules

B: Class II aldolase/adducin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3418
Polymers118,9574
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10670 Å2
ΔGint-82 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.407, 74.407, 179.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

21A-353-

HOH

31B-335-

HOH

41B-351-

HOH

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Components

#1: Protein Class II aldolase/adducin domain protein


Mass: 29739.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola 1448A (bacteria)
Strain: 1448A / Race 6 / Gene: PSPPH_2884 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q48HR6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4K 30%, Ammonium Acetate 0.2M, tri-Na-Citrate 0.1M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 37960 / Num. obs: 37674 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 40.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.665 / Num. unique all: 1808 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 9.405 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1882 5 %RANDOM
Rwork0.183 ---
all0.1858 39490 --
obs0.1858 37608 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 35.437 Å2 / Biso min: 18.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20 Å2
2---2.62 Å20 Å2
3---5.23 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 5 335 4192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214174
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9355706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99323.204206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48715658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9211538
X-RAY DIFFRACTIONr_chiral_restr0.0890.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213300
X-RAY DIFFRACTIONr_mcbond_it1.3551.52614
X-RAY DIFFRACTIONr_mcangle_it2.44224208
X-RAY DIFFRACTIONr_scbond_it2.53531560
X-RAY DIFFRACTIONr_scangle_it4.154.51498
X-RAY DIFFRACTIONr_rigid_bond_restr1.36434174
LS refinement shellResolution: 1.947→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 109 -
Rwork0.215 2491 -
all-2600 -
obs-2600 98.34 %
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)
10.40350.05980.08260.2880.04670.0867-0.00610.0136-0.0016-0.01780.00390.02310.00120.00870.00220.2215-0.0021-0.00060.2186-0.00040.202711.0898.71959.281
20.0895-0.03980.03380.07640.00190.0111-0.0001-0.00270.01170.003-0.00750.01170.005-0.00080.00760.2191-0.00060.00150.22-0.00080.204520.6213.78679.101
30.24040.3837-0.02910.96810.41280.6648-0.06670.11690.0916-0.07310.0940.02240.0144-0.0166-0.02730.225-0.0204-0.01220.26420.03420.210225.64317.41656.763
40.41640.18520.26830.6729-0.24720.6198-0.0328-0.05190.09310.0462-0.0018-0.008-0.0441-0.05640.03460.22770.0114-0.00320.2298-0.01130.177120.45322.03129.406
50.0744-0.1051-0.01890.1293-0.00780.0041-0.00680.00110.0115-0.00320.0030.0194-0.0034-0.00780.00380.2205-0.0002-0.00060.22160.00010.19619.6612.1919.757
60.20330.208-0.14420.83010.3360.38620.035-0.0154-0.03110.019-0.0217-0.025-0.0196-0.0271-0.01340.21770.0013-0.00320.2294-0.00150.191116.8295.48832.316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 246
3X-RAY DIFFRACTION3A247 - 271
4X-RAY DIFFRACTION4B1 - 105
5X-RAY DIFFRACTION5B106 - 246
6X-RAY DIFFRACTION6B247 - 271

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