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- PDB-4q52: 2.60 Angstrom resolution crystal structure of a conserved unchara... -

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Basic information

Entry
Database: PDB / ID: 4q52
Title2.60 Angstrom resolution crystal structure of a conserved uncharacterized protein from Chitinophaga pinensis DSM 2588
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / conserved uncharacterized protein
Function / homologyInclusion body protein / Uncharacterised protein family PixA/AidA / PixA-like superfamily / Inclusion body protein / Immunoglobulin-like / Sandwich / Mainly Beta / beta-D-glucopyranose / Uncharacterized protein
Function and homology information
Biological speciesChitinophaga pinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.60 Angstrom resolution crystal structure of a conserved uncharacterized protein from Chitinophaga pinensis DSM 2588
Authors: Halavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0307
Polymers82,4894
Non-polymers5403
Water4,125229
1
A: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6054
Polymers41,2452
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-29 kcal/mol
Surface area15160 Å2
MethodPISA
2
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4253
Polymers41,2452
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-34 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.712, 85.549, 88.195
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A23 - 197
2010B23 - 197
1020A23 - 197
2020C23 - 197
1030A23 - 197
2030D23 - 197
1040B23 - 197
2040C23 - 197
1050B23 - 197
2050D23 - 197
1060C23 - 197
2060D23 - 197

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Uncharacterized protein


Mass: 20622.350 Da / Num. of mol.: 4 / Fragment: UNP residues 21-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis (bacteria) / Strain: DSM 2588 / Gene: Cpin_5099 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic (SeMet) / References: UniProt: C7PQX8
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein: 7.8 mg/mL in 10 mM Tris/HCl, 500 mM NaCl, 5 mM BME crystallization: the PACT Suite (C11: 0.2 M CaCl2, 0.1 M HEPES pH 7.0, 20 % (w/v) PEG 6000) cryo: 25 % glucose, VAPOR DIFFUSION, ...Details: protein: 7.8 mg/mL in 10 mM Tris/HCl, 500 mM NaCl, 5 mM BME crystallization: the PACT Suite (C11: 0.2 M CaCl2, 0.1 M HEPES pH 7.0, 20 % (w/v) PEG 6000) cryo: 25 % glucose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2014 / Details: Be lenses
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 22847 / Num. obs: 22847 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1110 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.19 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.709 / SU ML: 0.204 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21529 1167 5.1 %RANDOM
Rwork0.16869 ---
obs0.17114 21649 99.53 %-
all-21649 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0 Å20.64 Å2
2---2.67 Å2-0 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 36 229 5571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025480
X-RAY DIFFRACTIONr_bond_other_d0.0060.025033
X-RAY DIFFRACTIONr_angle_refined_deg1.621.967502
X-RAY DIFFRACTIONr_angle_other_deg1.057311615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5395680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11625.268224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37715775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.075158
X-RAY DIFFRACTIONr_chiral_restr0.090.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216190
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021228
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A93700.08
12B93700.08
21A96110.08
22C96110.08
31A88900.09
32D88900.09
41B94140.08
42C94140.08
51B90550.07
52D90550.07
61C91110.08
62D91110.08
LS refinement shellResolution: 2.6→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 80 -
Rwork0.216 1524 -
obs-1524 96.16 %

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