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- PDB-2pjq: Crystal structure of Q88U62_LACPL from Lactobacillus plantarum. N... -

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Basic information

Entry
Database: PDB / ID: 2pjq
TitleCrystal structure of Q88U62_LACPL from Lactobacillus plantarum. Northeast Structural Genomics target LpR71
ComponentsUncharacterized protein lp_2664
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / LpR71 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


HD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / HD domain / HD domain / Cyclin A; domain 1 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Metal-dependent phosphohydrolase, HD family / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsBenach, J. / Su, M. / Seetharaman, J. / Forouhar, F. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Owens, L. / Baran, M. / Acton, T.B. ...Benach, J. / Su, M. / Seetharaman, J. / Forouhar, F. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Owens, L. / Baran, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Q88U62_LACPL from Lactobacillus plantarum.
Authors: Benach, J. / Su, M. / Seetharaman, J. / Forouhar, F. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Owens, L. / Baran, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Remark 300 BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). STATIC LIGHT SCATTERING DATA SHOWS THAT THIS PROTEIN IS A DIMER IN SOLUTION (10MM TRIS-HCL, 5MM DTT, 100MM NACL). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein lp_2664
B: Uncharacterized protein lp_2664
C: Uncharacterized protein lp_2664
D: Uncharacterized protein lp_2664


Theoretical massNumber of molelcules
Total (without water)104,9464
Polymers104,9464
Non-polymers00
Water21612
1
B: Uncharacterized protein lp_2664
C: Uncharacterized protein lp_2664


Theoretical massNumber of molelcules
Total (without water)52,4732
Polymers52,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-18 kcal/mol
Surface area19420 Å2
MethodPISA
2
A: Uncharacterized protein lp_2664

A: Uncharacterized protein lp_2664


Theoretical massNumber of molelcules
Total (without water)52,4732
Polymers52,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
3
D: Uncharacterized protein lp_2664

D: Uncharacterized protein lp_2664


Theoretical massNumber of molelcules
Total (without water)52,4732
Polymers52,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)79.928, 167.442, 63.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsStatic light scattering data shows a dimer, however there are two types of dimers in the AU.

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Components

#1: Protein
Uncharacterized protein lp_2664


Mass: 26236.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarumLactiplantibacillus plantarum
Strain: WCFS1, NCIMB 8826 / Gene: lp_2664 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q88U62, UniProt: F9URF4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 4
Details: 0.1M KNO3, 0.1M Na3 citrate pH 4.0, 40% PEG1000, MICROBATCH UNDER OIL, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97950, 0.97900, 0.95000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.9791
30.951
Reflection

D res high: 2.8 Å / D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
3.919.61568160.1311.364055899.7
3.928.71582090.1471.624103499.6
3.7310.11492500.131.754059299.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.810.0721.3434
4.796.0399.810.0981.2554.1
4.184.7910010.0961.2754.1
3.84.1810010.1141.4394
3.533.899.710.1351.4943.8
3.323.5399.910.1651.3693.8
3.153.3299.810.211.3423.8
3.023.1599.710.2631.3883.7
2.93.0299.110.3221.3793.7
2.82.998.910.4151.3393.6
6.035099.920.0741.3284
4.796.0310020.0951.3844.1
4.184.7910020.1061.4044.1
3.84.1899.820.1281.4833.9
3.533.899.520.1521.4453.8
3.323.5399.520.1971.5283.8
3.153.3299.720.2471.673.8
3.023.1599.220.3181.763.7
2.93.0299.320.3941.7863.7
2.82.998.920.5221.9163.7
6.035099.430.0721.2193.9
4.796.0399.930.0981.4294
4.184.7910030.0971.4284
3.84.1899.830.1191.9843.7
3.533.899.330.1341.7463.6
3.323.5399.230.1731.8353.6
3.153.3299.430.2181.9123.5
3.023.1599.230.2741.9433.5
2.93.0299.130.332.0073.5
2.82.998.630.4231.9693.4
ReflectionResolution: 2.8→50 Å / Num. obs: 41034 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.147 / Χ2: 1.62 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.93.70.52240971.91698.9
2.9-3.023.70.39440941.78699.3
3.02-3.153.70.31840511.7699.2
3.15-3.323.80.24741181.6799.7
3.32-3.533.80.19741201.52899.5
3.53-3.83.80.15240901.44599.5
3.8-4.183.90.12840971.48399.8
4.18-4.794.10.10641021.404100
4.79-6.034.10.09541291.384100
6.03-5040.07441361.32899.9

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.88 Å / D res low: 9.97 Å / FOM : 0.485 / Reflection: 16438
Phasing dmFOM : 0.69 / FOM acentric: 0.7 / FOM centric: 0.62 / Reflection: 19570 / Reflection acentric: 17010 / Reflection centric: 2560
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-47.8210.920.940.871017697320
5-80.810.830.6828702352518
4-50.820.840.6834803010470
3.5-40.780.790.6933162943373
3-3.50.610.620.4956755097578
2.8-30.430.450.332122911301

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / FOM work R set: 0.794 / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.307 3465 8.5 %
Rwork0.236 --
obs0.236 35367 87.1 %
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 32.079 Å2
Baniso -1Baniso -2Baniso -3
1-2.693 Å20 Å20 Å2
2---3.503 Å20 Å2
3---0.811 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6563 0 0 12 6575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012792
X-RAY DIFFRACTIONc_angle_deg1.61261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.820.238430.211476519
2.82-2.840.357640.266526590
2.84-2.860.357710.276495566
2.86-2.880.409690.307513582
2.88-2.90.438600.278551611
2.9-2.920.287690.269575644
2.92-2.940.367510.271527578
2.94-2.970.464610.272573634
2.97-2.990.374540.251580634
2.99-3.020.312770.247564641
3.02-3.040.305690.271587656
3.04-3.070.349610.236589650
3.07-3.090.217710.207579650
3.09-3.120.3620.235615677
3.12-3.150.384610.279600661
3.15-3.180.287770.241684761
3.18-3.210.247740.208587661
3.21-3.250.325620.254592654
3.25-3.280.318700.237639709
3.28-3.320.32860.258630716
3.32-3.360.336700.256648718
3.36-3.390.263690.235608677
3.39-3.440.31770.236629706
3.44-3.480.242660.192645711
3.48-3.520.316700.25649719
3.52-3.570.388530.24627680
3.57-3.620.342490.225667716
3.62-3.680.276850.249705790
3.68-3.730.369630.242660723
3.73-3.790.252830.227682765
3.79-3.860.292690.205632701
3.86-3.930.292610.234699760
3.93-40.302730.229658731
4-4.090.307720.205646718
4.09-4.170.279740.206708782
4.17-4.270.209880.18689777
4.27-4.380.333760.203680756
4.38-4.490.272860.22689775
4.49-4.620.279710.188701772
4.62-4.770.283610.2702763
4.77-4.940.374660.203713779
4.94-5.130.269800.209692772
5.13-5.360.336830.239700783
5.36-5.640.408680.285706774
5.64-5.980.459510.279712763
5.98-6.430.302830.29687770
6.43-7.050.346790.262699778
7.05-8.020.265790.228735814
8.02-9.890.272810.232706787
9.89-200.298670.283746813
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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