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- PDB-6qhn: Metagenome-derived salicylaldehyde dehydrogenase from alpine soil... -

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Basic information

Entry
Database: PDB / ID: 6qhn
TitleMetagenome-derived salicylaldehyde dehydrogenase from alpine soil in complex with protocatechuic acid
ComponentsSALICYLALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / salicylaldehyde dehydrogenase / metagenome / alpine soil / complex
Function / homology3,4-DIHYDROXYBENZOIC ACID
Function and homology information
Biological speciesAlphaproteobacteria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHakansson, M. / Svensson, L.A. / Shamsudeen, D.U. / Allen, C.C.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Expression, purification and crystallization of a novel metagenome-derived salicylaldehyde dehydrogenase from Alpine soil.
Authors: Dandare, S.U. / Hakansson, M. / Svensson, L.A. / Timson, D.J. / Allen, C.C.R.
History
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 2, 2022Group: Author supporting evidence / Structure summary / Category: pdbx_entity_instance_feature / pdbx_entry_details
Revision 1.3May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SALICYLALDEHYDE DEHYDROGENASE
B: SALICYLALDEHYDE DEHYDROGENASE
C: SALICYLALDEHYDE DEHYDROGENASE
D: SALICYLALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,2229
Polymers196,5144
Non-polymers7095
Water28,9861609
1
A: SALICYLALDEHYDE DEHYDROGENASE
C: SALICYLALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6575
Polymers98,2572
Non-polymers4003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-30 kcal/mol
Surface area32310 Å2
MethodPISA
2
B: SALICYLALDEHYDE DEHYDROGENASE
D: SALICYLALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5654
Polymers98,2572
Non-polymers3082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-29 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.839, 121.728, 318.048
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-934-

HOH

21D-888-

HOH

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Components

#1: Protein
SALICYLALDEHYDE DEHYDROGENASE


Mass: 49128.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alphaproteobacteria (bacteria) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical
ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1609 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6 and 8 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.9→29.89 Å / Num. obs: 177084 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 31.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.061 / Rrim(I) all: 0.144 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.935.71.648186060.3920.7581.81798.7
10.41-29.894.80.0452811460.9970.0220.0595.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å29.89 Å
Translation1.9 Å29.89 Å

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Processing

Software
NameVersionClassification
XDSJun 1, 2017data reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZ6

4jz6


Resolution: 1.9→27.67 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.205 8994 5.08 %RANDOM
Rwork0.18 ---
obs0.181 176985 99.9 %-
Displacement parametersBiso max: 183.02 Å2 / Biso mean: 37.33 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.1845 Å20 Å20 Å2
2---1.9674 Å20 Å2
3---1.7829 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.9→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13636 0 50 1614 15300
Biso mean--46.03 45.61 -
Num. residues----1864
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6163SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4552HARMONIC5
X-RAY DIFFRACTIONt_it28071HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1928SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact30259SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d28071HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg50881HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion13.92
LS refinement shellResolution: 1.9→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2494 172 4.86 %
Rwork0.2197 3368 -
all0.2212 3540 -
obs--97.46 %
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)
10.4478-0.08020.05630.33330.11520.49570.00410.007-0.0384-0.030.0756-0.11770.03290.0602-0.0797-0.03980.0376-0.0024-0.0264-0.0265-0.0449-16.4296-41.755531.0657
20.663-0.1020.08290.355-0.13730.4184-0.0415-0.04610.0772-0.03840.03570.0863-0.0603-0.05740.0058-0.030.0423-0.043-0.0418-0.0225-0.0546-0.9338-81.662228.6744
30.7179-0.01670.25850.4587-0.07370.41540.0844-0.2394-0.31380.0280.04430.03950.1386-0.1077-0.1287-0.07320.0093-0.0537-0.02530.1098-0.0526-42.6021-57.415648.1369
41.32170.15390.41220.36780.18880.7388-0.1018-0.47420.4028-0.0003-0.01010.036-0.1418-0.14080.112-0.13280.0981-0.04810.0013-0.1695-0.104120.3923-70.84953.9596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 470
2X-RAY DIFFRACTION2{ B|* }B5 - 470
3X-RAY DIFFRACTION3{ C|* }C5 - 470
4X-RAY DIFFRACTION4{ D|* }D5 - 470

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