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- PDB-3mnf: Crystal structure of PAC2 family protein from Streptomyces avermi... -

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Basic information

Entry
Database: PDB / ID: 3mnf
TitleCrystal structure of PAC2 family protein from Streptomyces avermitilis MA
ComponentsPAC2 family protein
Keywordsstructural genomics / unknown function / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyProtein of unknown function DUF774 / PAC-like subunit / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 Å
AuthorsChang, C. / Hatzos, C. / Morgan, T. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of PAC2 family protein from Streptomyces avermitilis MA
Authors: Chang, C. / Hatzos, C. / Morgan, T. / Bearden, J. / Joachimiak, A.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 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

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Assembly

Deposited unit
A: PAC2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4172
Polymers27,3811
Non-polymers351
Water0
1
A: PAC2 family protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,50012
Polymers164,2886
Non-polymers2136
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area15220 Å2
ΔGint-127 kcal/mol
Surface area61860 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)143.943, 143.943, 81.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Detailshexamer with operators (x,y,z), (-y+1,x-y,z), (-x+y+1,-x+1,z), (-y+1,-x+1,-z+1/2), (x,x-y,-z+1/2), (-x+y+1,y,-z+1/2)

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Components

#1: Protein PAC2 family protein


Mass: 27381.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: SAV6650, SAV_6650 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q828L9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 4.43 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0M Na/K tartrate, 0.1M MES, pH 6.0, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. all: 11041 / Num. obs: 10559 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 41.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 4.84 / Num. unique all: 507 / % possible all: 100

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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
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.97→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.919 / SU B: 26.757 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.5 / ESU R Free: 0.306
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24108 502 4.8 %RANDOM
Rwork0.21572 ---
all0.21696 10484 --
obs0.21696 10484 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.778 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å20 Å2
2---0.74 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 1 0 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9542459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3523.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27215246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4611512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211391
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_it0.541.51171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04621871
X-RAY DIFFRACTIONr_scbond_it1.5573619
X-RAY DIFFRACTIONr_scangle_it2.7164.5588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.975→3.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 28 -
Rwork0.236 668 -
obs-696 98.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.0159-1.74120.20983.58141.114.6110.2128-0.2480.09940.19270.06810.2842-0.1055-0.7718-0.28090.12130.07340.14230.20780.08790.210653.809255.719834.435
23.80023.219-3.51778.0211-1.92393.5528-0.01560.25350.05190.32380.10690.65450.1144-0.4026-0.09130.1507-0.0405-0.01930.34320.1940.459855.423737.720435.2197
34.4827-0.73770.95363.757-1.04513.94330.10740.20420.4282-0.21430.06480.1238-0.2607-0.5534-0.17220.15160.09520.11810.18950.05180.185457.063756.797827.1985
45.2642-1.1249-0.50342.89980.30934.94790.0327-0.60420.930.43140.254-0.1885-0.8988-0.2183-0.28670.40080.11240.16920.1759-0.10280.336761.190466.641140.5754
56.4154-0.68325.57756.31370.094913.36850.0383-1.63390.53151.79040.03691.1712-0.4417-1.4633-0.07520.76990.27520.46110.9917-0.11340.376149.318963.4455.2009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 52
2X-RAY DIFFRACTION2A53 - 75
3X-RAY DIFFRACTION3A76 - 119
4X-RAY DIFFRACTION4A120 - 214
5X-RAY DIFFRACTION5A215 - 256

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