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- PDB-4mxn: Crystal structure of a putative glycosyl hydrolase (PARMER_00599)... -

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Basic information

Entry
Database: PDB / ID: 4mxn
TitleCrystal structure of a putative glycosyl hydrolase (PARMER_00599) from Parabacteroides merdae ATCC 43184 at 1.95 A resolution
ComponentsUncharacterized protein
KeywordsHYDROLASE / Pectate_lyase_3 / PF12708 family / glycosyl hydrolase family 28 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


raffinose alpha-galactosidase activity / polygalacturonase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesParabacteroides merdae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (PARMER_00599) from Parabacteroides merdae ATCC 43184 at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,6024
Polymers107,6024
Non-polymers00
Water7,855436
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9011
Polymers26,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9011
Polymers26,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9011
Polymers26,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9011
Polymers26,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.650, 62.430, 67.960
Angle α, β, γ (deg.)90.890, 118.340, 100.630
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein


Mass: 26900.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Gene: PARMER_00599 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AB45
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (23-250) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 1.92 Å3/Da / Density % sol: 35.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.200M magnesium chloride, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97879
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 1.95→48.659 Å / Num. obs: 53539 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / Biso Wilson estimate: 23.832 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-23.590.5882.1914052391291.4
2-2.060.4852.713265368587.7
2.06-2.120.4083.214101382793.3
2.12-2.180.3413.814182380194.4
2.18-2.250.294.513388359294.1
2.25-2.330.2485.212843348693.2
2.33-2.420.2136.112168329591.8
2.42-2.520.181710871298186.1
2.52-2.630.1448.811828315294.8
2.63-2.760.12310.211256298494.6
2.76-2.910.09912.310638283792.9
2.91-3.080.07615.49755260391.2
3.08-3.30.05619.68502228585.2
3.3-3.560.04424.49016238894.3
3.56-3.90.03828.67993212693.6
3.9-4.360.03331.47145190290.9
4.36-5.030.02933.65732154484.1
5.03-6.170.039305591147394.5
6.17-8.720.03932.74036107390.1
8.72-48.660.02844.6221359388.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.95→48.659 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9214 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 2717 5.08 %RANDOM
Rwork0.1828 ---
obs0.1844 53533 91.88 %-
Displacement parametersBiso max: 130.37 Å2 / Biso mean: 29.3334 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.3134 Å20.2353 Å20.592 Å2
2---4.2647 Å21.7261 Å2
3---3.9513 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å
Refinement stepCycle: LAST / Resolution: 1.95→48.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6667 0 0 436 7103
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3335SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes195HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1050HARMONIC5
X-RAY DIFFRACTIONt_it6926HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion961SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8453SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6926HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9391HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion2.66
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2525 195 4.99 %
Rwork0.1954 3711 -
all0.1983 3906 -
obs--91.88 %
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)
11.07830.18090.57990.34320.22812.1868-0.0324-0.011-0.1155-0.07650.04770.0206-0.0078-0.1072-0.0154-0.065-0.0125-0.0087-0.0682-0.0031-0.0137-0.88251.187712.6581
21.1811-0.2549-0.00810.3194-0.181.70080.02370.03890.0021-0.0231-0.0040.045-0.0787-0.0305-0.0197-0.0192-0.00280.0075-0.0689-0.0124-0.0451-5.647234.9847-16.3596
31.2094-0.0921-0.14450.597-0.66922.4652-0.0975-0.1245-0.01490.06980.0668-0.01210.0411-0.39620.0306-0.0854-0.0013-0.0052-0.03-0.0341-0.060731.33084.9341-11.8278
41.18540.13790.66510.31650.08542.0157-0.0080.14310.04810.0316-0.0044-0.0163-0.03640.27280.0124-0.0604-0.01250.0162-0.027-0.001-0.057419.856530.94778.5951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|23-A|247 }
2X-RAY DIFFRACTION2{ B|23-B|247 }
3X-RAY DIFFRACTION3{ C| 0-C|244 }
4X-RAY DIFFRACTION4{ D|23-D|250 }

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