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- PDB-3ilm: Crystal Structure of the Alr3790 protein from Anabaena sp. Northe... -

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Basic information

Entry
Database: PDB / ID: 3ilm
TitleCrystal Structure of the Alr3790 protein from Anabaena sp. Northeast Structural Genomics Consortium Target NsR437h
ComponentsAlr3790 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alr3790 / Rhodanese-like / NsR437h / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.262 Å
AuthorsVorobiev, S. / Chen, Y. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Alr3790 protein from Anabaena sp.
Authors: Vorobiev, S. / Chen, Y. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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: Alr3790 protein
B: Alr3790 protein
C: Alr3790 protein
D: Alr3790 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8829
Polymers63,6074
Non-polymers2755
Water2,684149
1
A: Alr3790 protein
B: Alr3790 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9144
Polymers31,8042
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-30 kcal/mol
Surface area11190 Å2
MethodPISA
2
C: Alr3790 protein
D: Alr3790 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9695
Polymers31,8042
Non-polymers1653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-38 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.694, 77.293, 156.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alr3790 protein


Mass: 15901.864 Da / Num. of mol.: 4 / Fragment: sequence database residues 20-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr3790 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q8YQN0
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 39.53 %
Crystal growTemperature: 277 K / Method: microbatch under parafin oil / pH: 6
Details: 20% PEG 1000, 0.1M manganese chloride, 0.1M MES, pH 6.0, microbatch under parafin oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2009 / Details: FLAT COLLIMATING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. all: 46780 / Num. obs: 46546 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 36.82 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 19.4
Reflection shellResolution: 2.26→2.35 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4660 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SnBphasing
RESOLVEmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.262→41.195 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 28.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 2372 5.1 %RANDOM
Rwork0.232 ---
obs0.2327 46479 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.734 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.0511 Å20 Å2-0 Å2
2--26.5038 Å2-0 Å2
3----14.4527 Å2
Refinement stepCycle: LAST / Resolution: 2.262→41.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 5 149 3868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073780
X-RAY DIFFRACTIONf_angle_d1.4415105
X-RAY DIFFRACTIONf_dihedral_angle_d20.481349
X-RAY DIFFRACTIONf_chiral_restr0.095564
X-RAY DIFFRACTIONf_plane_restr0.008671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.262-2.30810.32861320.32482425X-RAY DIFFRACTION95
2.3081-2.35830.34081530.31392567X-RAY DIFFRACTION98
2.3583-2.41320.35071270.30892598X-RAY DIFFRACTION99
2.4132-2.47350.31911200.29632581X-RAY DIFFRACTION99
2.4735-2.54040.26941340.2892625X-RAY DIFFRACTION99
2.5404-2.61510.30621370.26522617X-RAY DIFFRACTION100
2.6151-2.69950.27911440.25992606X-RAY DIFFRACTION100
2.6995-2.7960.32491370.2482602X-RAY DIFFRACTION100
2.796-2.90790.26781310.2612640X-RAY DIFFRACTION100
2.9079-3.04020.31671500.2562625X-RAY DIFFRACTION100
3.0402-3.20040.35191400.2562565X-RAY DIFFRACTION100
3.2004-3.40090.27121310.23132635X-RAY DIFFRACTION100
3.4009-3.66330.19911400.20772602X-RAY DIFFRACTION100
3.6633-4.03170.19111570.17982582X-RAY DIFFRACTION100
4.0317-4.61440.16531520.16362626X-RAY DIFFRACTION100
4.6144-5.8110.18911580.1792586X-RAY DIFFRACTION100
5.811-41.20170.20441290.23422625X-RAY DIFFRACTION100
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)
10.67350.26150.23651.2049-0.81581.1712-0.0460.00920.03230.06230.014-0.06870.12210.0066-00.06580.0115-0.00220.0626-0.04680.095828.842428.841273.8941
20.626-0.745-0.17440.1384-0.59871.3943-0.0257-0.090.06090.02180.016-0.0726-0.1320.100900.1655-0.0086-0.01060.1818-0.0390.187125.666940.07553.4853
30.366-1.059-0.11831.4983-0.89371.022-0.06630.12980.0010.1028-0.0231-0.00520.0828-0.4235-00.137-0.02880.0040.2674-0.05020.148620.674147.7308110.3494
40.0686-0.4812-0.67261.61590.34231.1709-0.0243-0.0092-0.0059-0.0720.05920.0276-0.01510.4707-00.17230.0474-0.00350.2178-0.04970.135437.531649.601693.1377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA20 - 144
2X-RAY DIFFRACTION2chain BB20 - 156
3X-RAY DIFFRACTION3chain CC20 - 156
4X-RAY DIFFRACTION4chain DD20 - 156

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