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- PDB-4e1y: Alginate lyase A1-III H192A apo form -

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Basic information

Entry
Database: PDB / ID: 4e1y
TitleAlginate lyase A1-III H192A apo form
ComponentsAlginate lyase
KeywordsLYASE / ALPHA BARREL / polysaccharide LYASE / ALGINATE
Function / homology
Function and homology information


periplasmic space / lyase activity
Similarity search - Function
Alginate lyase domain / Alginate lyase / Alginate lyase 2 / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Glycosyltransferase / Alpha/alpha barrel / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSphingomonas (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMikami, B. / Ban, M. / Suzuki, S. / Yoon, H.-J. / Miyake, O. / Yamasaki, M. / Ogura, K. / Maruyama, Y. / Hashimoto, W. / Murata, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III
Authors: Mikami, B. / Ban, M. / Suzuki, S. / Yoon, H.-J. / Miyake, O. / Yamasaki, M. / Ogura, K. / Maruyama, Y. / Hashimoto, W. / Murata, K.
History
DepositionMar 7, 2012Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 11, 2012ID: 3EVH
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Nov 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase
B: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)79,5072
Polymers79,5072
Non-polymers00
Water5,170287
1
A: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)39,7541
Polymers39,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)39,7541
Polymers39,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.443, 76.990, 143.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISPHEPHEchain A and (resseq 6:8 or resseq 11:13 or resseq...AA6 - 83 - 5
12ALAALAVALVALchain A and (resseq 6:8 or resseq 11:13 or resseq...AA11 - 138 - 10
13ASPASPGLNGLNchain A and (resseq 6:8 or resseq 11:13 or resseq...AA15 - 3112 - 28
14LEULEUPROPROchain A and (resseq 6:8 or resseq 11:13 or resseq...AA35 - 4432 - 41
15GLUGLUPROPROchain A and (resseq 6:8 or resseq 11:13 or resseq...AA46 - 6543 - 62
16ARGARGASNASNchain A and (resseq 6:8 or resseq 11:13 or resseq...AA67 - 7264 - 69
17GLYGLYSERSERchain A and (resseq 6:8 or resseq 11:13 or resseq...AA74 - 13571 - 132
18TYRTYRPROPROchain A and (resseq 6:8 or resseq 11:13 or resseq...AA137 - 157134 - 154
19VALVALHISHISchain A and (resseq 6:8 or resseq 11:13 or resseq...AA159 - 177156 - 174
110PROPROTRPTRPchain A and (resseq 6:8 or resseq 11:13 or resseq...AA182 - 195179 - 192
111GLYGLYASPASPchain A and (resseq 6:8 or resseq 11:13 or resseq...AA197 - 210194 - 207
112LEULEUPHEPHEchain A and (resseq 6:8 or resseq 11:13 or resseq...AA212 - 308209 - 305
113PROPROPROPROchain A and (resseq 6:8 or resseq 11:13 or resseq...AA310 - 354307 - 351
21HISHISPHEPHEchain B and (resseq 6:8 or resseq 11:13 or resseq...BB6 - 83 - 5
22ALAALAVALVALchain B and (resseq 6:8 or resseq 11:13 or resseq...BB11 - 138 - 10
23ASPASPGLNGLNchain B and (resseq 6:8 or resseq 11:13 or resseq...BB15 - 3112 - 28
24LEULEUPROPROchain B and (resseq 6:8 or resseq 11:13 or resseq...BB35 - 4432 - 41
25GLUGLUPROPROchain B and (resseq 6:8 or resseq 11:13 or resseq...BB46 - 6543 - 62
26ARGARGASNASNchain B and (resseq 6:8 or resseq 11:13 or resseq...BB67 - 7264 - 69
27GLYGLYSERSERchain B and (resseq 6:8 or resseq 11:13 or resseq...BB74 - 13571 - 132
28TYRTYRPROPROchain B and (resseq 6:8 or resseq 11:13 or resseq...BB137 - 157134 - 154
29VALVALHISHISchain B and (resseq 6:8 or resseq 11:13 or resseq...BB159 - 177156 - 174
210PROPROTRPTRPchain B and (resseq 6:8 or resseq 11:13 or resseq...BB182 - 195179 - 192
211GLYGLYASPASPchain B and (resseq 6:8 or resseq 11:13 or resseq...BB197 - 210194 - 207
212LEULEUPHEPHEchain B and (resseq 6:8 or resseq 11:13 or resseq...BB212 - 308209 - 305
213PROPROPROPROchain B and (resseq 6:8 or resseq 11:13 or resseq...BB310 - 354307 - 351

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Components

#1: Protein Alginate lyase


Mass: 39753.676 Da / Num. of mol.: 2 / Fragment: UNP residues 54-404 / Mutation: H192A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas (bacteria) / Strain: A1 / Gene: aly / Plasmid: PISA412 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): 1423
References: UniProt: Q9KWU1, mannuronate-specific alginate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24%(W/V) PEG4000, 0.3M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 2, 2001 / Details: CARBON MONOCLOMETER
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40.634 Å / Num. all: 43099 / Num. obs: 41806 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 4.45 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 12.1
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 6213 / Rsym value: 0.298 / % possible all: 93.2

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Processing

Software
NameVersionClassification
FRAMBOdata collection
CNSrefinement
PHENIX(phenix.refine: 1.6.4_486)refinement
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAZ

1qaz


Resolution: 2.1→40.634 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8324 / SU ML: 0.24 / Cross valid method: throughou / σ(F): 0 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 2111 5.05 %RANDOM
Rwork0.1631 ---
obs0.1653 41806 96.98 %-
all-43108 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.817 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 144.11 Å2 / Biso mean: 31.3147 Å2 / Biso min: 5.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.8742 Å2-0 Å20 Å2
2---0.9666 Å20 Å2
3---0.0924 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 2.1→40.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 0 287 5887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125842
X-RAY DIFFRACTIONf_angle_d1.3267944
X-RAY DIFFRACTIONf_chiral_restr0.086838
X-RAY DIFFRACTIONf_plane_restr0.0071048
X-RAY DIFFRACTIONf_dihedral_angle_d15.5912182
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2584X-RAY DIFFRACTIONPOSITIONAL0.092
12B2584X-RAY DIFFRACTIONPOSITIONAL0.092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.36741200.28712481260192
2.1489-2.20260.27521150.24632548266393
2.2026-2.26210.30241250.23312544266994
2.2621-2.32870.30591250.21482540266595
2.3287-2.40390.25911370.19922587272495
2.4039-2.48980.25461480.18472545269396
2.4898-2.58940.23871360.18762594273096
2.5894-2.70730.26651550.18212617277297
2.7073-2.84990.21521390.18642680281998
2.8499-3.02850.22771510.17142658280999
3.0285-3.26220.19191500.168827382888100
3.2622-3.59030.1971530.140727212874100
3.5903-4.10940.15921550.123527572912100
4.1094-5.17570.12741430.109227892932100
5.1757-40.64120.16221590.13822896305599

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