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- PDB-4f9j: Structure of Escherichia coli PgaB 42-655 in complex with iron -

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Basic information

Entry
Database: PDB / ID: 4f9j
TitleStructure of Escherichia coli PgaB 42-655 in complex with iron
ComponentsPoly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
KeywordsHYDROLASE / Family 4 carbohydrate esterase / Tim barrel / carbohydrate/sugar binding / deacetylase
Function / homology
Function and homology information


macromolecule deacylation / cell adhesion involved in biofilm formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / single-species biofilm formation / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity, hydrolyzing O-glycosyl compounds / cell outer membrane / carbohydrate metabolic process
Similarity search - Function
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases ...Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.103 Å
AuthorsLittle, D.J. / Poloczek, J. / Whitney, J.C. / Robinson, H. / Nitz, M. / Howell, P.L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Structure and Metal Dependent Activity of Escherichia coli PgaB Provides Insight into the Partial De-N-acetylation of Poly-b-1,6-N-acetyl-D-glucosamine
Authors: Little, D.J. / Poloczek, J. / Whitney, J.C. / Robinson, H. / Nitz, M. / Howell, P.L.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
B: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,36210
Polymers143,6592
Non-polymers7028
Water11,908661
1
A: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1815
Polymers71,8301
Non-polymers3514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1815
Polymers71,8301
Non-polymers3514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.055, 102.428, 150.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase / PGA N-deacetylase / Poly-beta-1 / 6-GlcNAc N-deacetylase


Mass: 71829.727 Da / Num. of mol.: 2 / Fragment: UNP residues 42-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pgaB, ycdR, b1023, JW5142 / Production host: Escherichia coli (E. coli)
References: UniProt: P75906, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 669 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.45 Å3/Da / Density % sol: 49.78 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 82493 / Num. obs: 82493 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.103→45.528 Å / SU ML: 0.2 / σ(F): 4.82 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 1999 2.49 %RANDOM
Rwork0.1651 ---
obs0.1659 80411 97.27 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.99 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4668 Å20 Å2-0 Å2
2--6.4023 Å20 Å2
3----2.9356 Å2
Refinement stepCycle: LAST / Resolution: 2.103→45.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9506 0 36 661 10203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079824
X-RAY DIFFRACTIONf_angle_d1.03513393
X-RAY DIFFRACTIONf_dihedral_angle_d14.3753502
X-RAY DIFFRACTIONf_chiral_restr0.0711445
X-RAY DIFFRACTIONf_plane_restr0.0041729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.103-2.15510.26871300.19615101X-RAY DIFFRACTION90
2.1551-2.21340.20721380.17975400X-RAY DIFFRACTION95
2.2134-2.27850.23511390.17445443X-RAY DIFFRACTION96
2.2785-2.35210.2121400.17015492X-RAY DIFFRACTION97
2.3521-2.43610.21071400.16625523X-RAY DIFFRACTION97
2.4361-2.53370.21861410.16655548X-RAY DIFFRACTION97
2.5337-2.6490.22181440.16115610X-RAY DIFFRACTION98
2.649-2.78860.18071430.1665608X-RAY DIFFRACTION98
2.7886-2.96330.21591440.16755638X-RAY DIFFRACTION99
2.9633-3.1920.20071450.17165715X-RAY DIFFRACTION99
3.192-3.51320.19981470.15895732X-RAY DIFFRACTION99
3.5132-4.02130.16051460.15465755X-RAY DIFFRACTION100
4.0213-5.06530.17441490.13975836X-RAY DIFFRACTION99
5.0653-45.5280.20431530.18766011X-RAY DIFFRACTION99
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)
11.4263-0.2586-0.27981.24881.09752.9519-0.1661-0.441-0.01320.24660.15560.1599-0.05520.12140.00370.180.07610.01140.26630.03010.1320.761958.0961102.2204
21.6795-0.0388-0.43040.73730.20851.3565-0.024-0.0408-0.029-0.0340.0764-0.0813-0.01290.0298-0.04920.10530.0136-0.02060.1039-0.02060.145341.742557.276376.7749
32.7726-0.1547-0.13290.13390.1422.15850.0005-0.34-0.00110.06020.1064-0.08720.01170.2989-0.08730.177-0.0110.00690.1709-0.0450.203957.219861.452283.978
41.27760.09260.14381.1114-1.23713.7939-0.07830.3745-0.0139-0.18960.0263-0.0807-0.08520.06340.04130.1639-0.0398-0.00320.2457-0.03190.142970.221558.7022121.021
52.2986-0.1445-0.03220.3486-0.35851.041-0.00080.0985-0.16070.01570.0610.05530.0327-0.0293-0.04090.1356-0.0214-0.00570.0867-0.00460.169446.29959.8108145.8236
65.4886-0.00460.24630.4561.00072.6237-0.04850.2553-0.5246-0.0657-0.00010.06350.2214-0.52120.04050.2095-0.04090.00750.3081-0.01880.219731.32255.8831134.8214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 43:282 )A43 - 282
2X-RAY DIFFRACTION2( CHAIN A AND RESID 283:529 )A283 - 529
3X-RAY DIFFRACTION3( CHAIN A AND RESID 530:649 )A530 - 649
4X-RAY DIFFRACTION4( CHAIN B AND RESID 43:282 )B43 - 282
5X-RAY DIFFRACTION5( CHAIN B AND RESID 283:596 )B283 - 596
6X-RAY DIFFRACTION6( CHAIN B AND RESID 597:649 )B597 - 649

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