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- PDB-4qfu: Crystal structure of a glycoside hydrolase family 5 (BVU_2644) fr... -

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Entry
Database: PDB / ID: 4qfu
TitleCrystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution
Componentsglycoside hydrolase family 5
KeywordsHYDROLASE / putative catalytic domain / TIM barrel fold / PF13204 family / beta-sandwich fold / PF12904 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Putative collagen-binding domain / Putative collagen-binding domain of a collagenase / Putative glycohydrolase domain DUF4038 / Protein of unknown function (DUF4038) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / SARCOSINE / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycoside hydrolase family 5
B: glycoside hydrolase family 5
C: glycoside hydrolase family 5
D: glycoside hydrolase family 5
E: glycoside hydrolase family 5
F: glycoside hydrolase family 5
G: glycoside hydrolase family 5
H: glycoside hydrolase family 5
I: glycoside hydrolase family 5
J: glycoside hydrolase family 5
K: glycoside hydrolase family 5
L: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)685,78354
Polymers682,06812
Non-polymers3,71542
Water95,8945323
1
A: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1114
Polymers56,8391
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1735
Polymers56,8391
Non-polymers3344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0824
Polymers56,8391
Non-polymers2433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1114
Polymers56,8391
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2916
Polymers56,8391
Non-polymers4525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1735
Polymers56,8391
Non-polymers3344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2005
Polymers56,8391
Non-polymers3614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1114
Polymers56,8391
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1114
Polymers56,8391
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1114
Polymers56,8391
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2005
Polymers56,8391
Non-polymers3614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: glycoside hydrolase family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1114
Polymers56,8391
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.950, 117.589, 125.249
Angle α, β, γ (deg.)91.600, 92.820, 98.920
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
glycoside hydrolase family 5 /


Mass: 56839.027 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_2644 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6L3N2

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Non-polymers , 5 types, 5365 molecules

#2: Chemical...
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-SAR / SARCOSINE / Sarcosine


Type: peptide linking / Mass: 89.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5323 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT (25-489) 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.17M magnesium nitrate, 18.0% polyethylene glycol 3350, 0.01M Sarcosine, 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: 0.91837,0.97932,0.97885
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.978851
ReflectionResolution: 1.9→46.868 Å / Num. obs: 459821 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.214 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.4152.19829442659180.9
1.97-2.050.3092.811368847999192.6
2.05-2.140.2383.710731145351191.7
2.14-2.250.1874.610631445013189.7
2.25-2.390.1465.710302543586185.1
2.39-2.580.126.911674249128192.9
2.58-2.840.088911146847015191.5
2.84-3.250.06112.610607945091188.2
3.25-4.080.04416.811011846988192.6
4.08-46.8680.04119.110757446400189.4

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Phasing

PhasingMethod: molecular replacement, MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
PHASER2.3.0phasing
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: molecular replacement, MAD / Resolution: 1.9→46.868 Å / Cor.coef. Fo:Fc: 0.9638 / Cor.coef. Fo:Fc free: 0.9512 / Occupancy max: 1 / Occupancy min: 0.23 / 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 MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. CL, SAR AND MRD MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 22984 5 %RANDOM
Rwork0.1422 ---
obs0.1437 459820 89.45 %-
Displacement parametersBiso max: 138.42 Å2 / Biso mean: 30.072 Å2 / Biso min: 10.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20.5143 Å21.5002 Å2
2--2.3544 Å21.5978 Å2
3----1.0345 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45399 0 234 5323 50956
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d21457SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes1311HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6945HARMONIC5
X-RAY DIFFRACTIONt_it47460HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5720SEMIHARMONIC5
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_contact58662SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d47460HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg64436HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion2.74
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2173 1336 4.73 %
Rwork0.1936 26922 -
all0.1947 28258 -
obs--89.45 %
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)
10.49450.0238-0.13310.5910.10590.3447-0.0019-0.03620.00780.0653-0.00880.08590.0661-0.03570.0107-0.0157-0.0131-0.008-0.06570.0016-0.01-82.7786-62.170656.5283
20.3232-0.0374-0.14480.49870.1030.4179-0.0196-0.02510.0180.01180.0181-0.018-0.07070.03260.0014-0.0012-0.00830.001-0.05560.0103-0.0179-53.7584-106.280150.2858
30.3445-0.21070.01050.8831-0.05170.44630.03270.0646-0.0296-0.1735-0.0231-0.0251-0.01560.021-0.0096-0.0167-0.00580.0026-0.0485-0.0004-0.0362-61.9743-29.554422.7417
40.56780.08150.3320.64780.01040.91-0.04210.1241-0.045-0.06130.0948-0.0665-0.1760.2236-0.0528-0.0595-0.07250.0453-0.0169-0.047-0.0747-78.7182-63.1934-2.6322
50.3936-0.13040.07310.79480.29290.56330.0136-0.00380.02130.15110.0425-0.25680.07860.0957-0.0561-0.06020.0108-0.0917-0.08650.00620.0374-38.868-36.8966.0123
60.7014-0.09630.26250.48530.05390.99260.0728-0.0276-0.119-0.02560.0020.03380.2789-0.0564-0.07480.0017-0.0268-0.0209-0.11660.0139-0.0381-94.9704-110.8856-10.9951
70.6394-0.25790.12270.5880.15250.60860.0204-0.15040.00240.22430.0113-0.00230.1055-0.0441-0.03170.0504-0.0387-0.003-0.07410.0205-0.1024-54.1342-130.130293.7292
81.0892-0.05020.04410.27790.08920.63170.0234-0.21650.06350.0919-0.0182-0.00320.075-0.0559-0.0052-0.0518-0.04130.0232-0.0258-0.0117-0.0571-110.4951-86.64830.0301
90.445-0.1389-0.09621.34610.530.46580.06570.0658-0.1059-0.1931-0.20110.3886-0.0985-0.150.1354-0.09470.0386-0.0448-0.0757-0.05870.0315-92.402-138.090459.7446
100.6353-0.36170.03570.72150.03660.65250.07360.14420.0044-0.1966-0.05130.06060.0181-0.1247-0.0223-0.04930.0094-0.0165-0.01350.0274-0.0761-10.9226-88.402882.0402
110.42620.0278-0.05510.4677-0.28580.75450.02930.11050.0340.0047-0.04060.11380.0357-0.2680.0113-0.1449-0.01410.04040.0726-0.0241-0.0318-32.4363-85.5969-1.0811
120.93230.05430.4930.50860.13721.0547-0.1316-0.18630.1578-0.00760.04810.0606-0.4637-0.24640.08350.07390.1332-0.0121-0.124-0.016-0.1094-12.7219-47.2039113.5436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|25 - 489}A25 - 489
2X-RAY DIFFRACTION2{B|-8 - 488}B-8 - 488
3X-RAY DIFFRACTION3{C|26 - 488}C26 - 488
4X-RAY DIFFRACTION4{D|25 - 489}D25 - 489
5X-RAY DIFFRACTION5{E|-8 - 489}E-8 - 489
6X-RAY DIFFRACTION6{F|-8 - 488}F-8 - 489
7X-RAY DIFFRACTION7{G|25 - 489}G25 - 489
8X-RAY DIFFRACTION8{H|26 - 489}H26 - 489
9X-RAY DIFFRACTION9{I|25 - 489}I25 - 489
10X-RAY DIFFRACTION10{J|26 - 488}J26 - 488
11X-RAY DIFFRACTION11{K|26 - 488}K26 - 488
12X-RAY DIFFRACTION12{L|26 - 488}L26 - 488

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