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- PDB-4r4z: Structure of PNGF-II in P21 space group -

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Basic information

Entry
Database: PDB / ID: 4r4z
TitleStructure of PNGF-II in P21 space group
ComponentsPNGF-II
KeywordsHYDROLASE / N-glycanase (PNGase) / PNGase F / Deglycosylation / N-glycoproteins
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen / metal ion binding
Similarity search - Function
Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal ...Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSun, G. / Yu, X. / Celimuge / Wang, L. / Li, M. / Gan, J. / Qu, D. / Ma, J. / Chen, L.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Identification and Characterization of a Novel Prokaryotic Peptide: N-glycosidase from Elizabethkingia meningoseptica
Authors: Sun, G. / Yu, X. / Celimuge / Wang, L. / Li, M. / Gan, J. / Qu, D. / Ma, J. / Chen, L.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PNGF-II
B: PNGF-II
C: PNGF-II
D: PNGF-II


Theoretical massNumber of molelcules
Total (without water)244,1224
Polymers244,1224
Non-polymers00
Water19811
1
A: PNGF-II


Theoretical massNumber of molelcules
Total (without water)61,0301
Polymers61,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PNGF-II


Theoretical massNumber of molelcules
Total (without water)61,0301
Polymers61,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PNGF-II


Theoretical massNumber of molelcules
Total (without water)61,0301
Polymers61,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PNGF-II


Theoretical massNumber of molelcules
Total (without water)61,0301
Polymers61,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.8, 94.2, 165.8
Angle α, β, γ (deg.)90.0, 91.4, 90.0
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
1010A11 - 549
2010B11 - 549
1020A11 - 549
2020C11 - 549
1030A11 - 548
2030D11 - 548
1040B11 - 549
2040C11 - 549
1050B11 - 547
2050D11 - 547
1060C11 - 547
2060D11 - 547

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
PNGF-II


Mass: 61030.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Strain: FMS-007 / Gene: CP006576 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: A0A090KI56*PLUS, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG3350, 0.1M sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289 K

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Data collection

DiffractionMean temperature: 196 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 60898 / Num. obs: 55844 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 9.87
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.28 / Num. unique all: 6029 / Rsym value: 0.42 / % possible all: 82

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R4X

4r4x


Resolution: 2.81→29.5 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.863 / SU B: 42.517 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2856 5.1 %RANDOM
Rwork0.199 ---
all0.204 60898 --
obs0.204 52973 90.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.349 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å2-0 Å20.96 Å2
2--5.75 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17023 0 0 11 17034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01917394
X-RAY DIFFRACTIONr_bond_other_d0.0030.0216504
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.94423553
X-RAY DIFFRACTIONr_angle_other_deg1.469338037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76552149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3325.742836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.745153040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0061552
X-RAY DIFFRACTIONr_chiral_restr0.0630.22583
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02120023
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024061
X-RAY DIFFRACTIONr_rigid_bond_restr8.198333898
X-RAY DIFFRACTIONr_sphericity_free71.81858
X-RAY DIFFRACTIONr_sphericity_bonded12.975533550
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A331940.07
12B331940.07
21A334930.06
22C334930.06
31A332840.06
32D332840.06
41B332830.07
42C332830.07
51B336410.06
52D336410.06
61C333790.07
62D333790.07
LS refinement shellResolution: 2.815→2.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 166 -
Rwork0.328 3156 -
obs--74.1 %
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)
12.5403-0.970.1490.9638-0.66332.28820.10680.21360.1845-0.18320.0343-0.0351-0.1291-0.0375-0.14110.0927-0.0360.00450.04820.03040.0561-70.968-10.687-79.797
20.76770.098-0.05150.78150.27980.8046-0.02660.0362-0.07380.1209-0.00860.02840.0708-0.06740.03530.08640.04790.01050.0588-0.00090.0702-36.1611-27.4987-56.0111
30.68020.15910.01520.8895-0.00072.2090.11580.0565-0.02050.3288-0.0873-0.11590.12170.1166-0.02850.28430.0533-0.05310.05720.00810.091-38.561-4.948-23.498
40.8480.0744-0.21030.77820.10251.0392-0.00660.19660.2296-0.0661-0.01370.0153-0.23110.00520.02030.13320.0259-0.03060.06950.05230.0786-31.45190.1754-66.2176
50.4860.04490.05423.31340.46450.71520.0071-0.0144-0.17570.0214-0.0960.26530.1485-0.11610.08890.0764-0.04430.08180.0629-0.08150.23597.597-17.819-38.944
61.397-0.29110.1540.77640.19680.62320.00230.26410.1394-0.0524-0.08070.0809-0.03770.02370.07850.22970.03610.00610.05650.03150.12380.627224.96-33.2797
70.83470.8661-1.01621.7117-1.03131.43620.1149-0.04340.04220.11920.00410.0734-0.12720.0504-0.11890.28250.0144-0.03180.0127-0.0330.20140.43936.119-20.064
81.6885-0.2199-0.0530.67560.12951.0143-0.0341-0.1021-0.15670.1562-0.01910.11360.048-0.07670.05310.2510.03740.06240.02620.03460.19455.56078.6917-8.6315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 201
2X-RAY DIFFRACTION2A202 - 540
3X-RAY DIFFRACTION3B11 - 201
4X-RAY DIFFRACTION4B202 - 539
5X-RAY DIFFRACTION5C11 - 201
6X-RAY DIFFRACTION6C202 - 539
7X-RAY DIFFRACTION7D11 - 201
8X-RAY DIFFRACTION8D202 - 538

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