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- PDB-5yln: Zinc dependent alcohol dehydrogenase 2 from Streptococcus pneumon... -

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Basic information

Entry
Database: PDB / ID: 5yln
TitleZinc dependent alcohol dehydrogenase 2 from Streptococcus pneumonia - apo form
ComponentsAlcohol dehydrogenase, zinc-containing
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / ADH
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Alcohol dehydrogenase, zinc-containing
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 Å
AuthorsDonghyuk, S. / Seungsu, H. / Sangho, L.
CitationJournal: To Be Published
Title: Zinc dependent alcohol dehydrogenase 2 from Streptococcus pneumonia - apo form
Authors: Donghyuk, S. / Seungsu, H. / Sangho, L.
History
DepositionOct 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase, zinc-containing
B: Alcohol dehydrogenase, zinc-containing
C: Alcohol dehydrogenase, zinc-containing
D: Alcohol dehydrogenase, zinc-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,94816
Polymers153,9374
Non-polymers1,01212
Water1,928107
1
A: Alcohol dehydrogenase, zinc-containing
B: Alcohol dehydrogenase, zinc-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4748
Polymers76,9682
Non-polymers5066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-92 kcal/mol
Surface area27980 Å2
MethodPISA
2
C: Alcohol dehydrogenase, zinc-containing
D: Alcohol dehydrogenase, zinc-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4748
Polymers76,9682
Non-polymers5066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-91 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.177, 123.245, 130.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alcohol dehydrogenase, zinc-containing /


Mass: 38484.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: SPD_1865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZRI0, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Tris-HCl, pH 8.0 PEG 3000 15%(v/v), 50 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.28277 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28277 Å / Relative weight: 1
ReflectionResolution: 2.189→47.098 Å / Num. obs: 73418 / % possible obs: 99 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09349 / Rrim(I) all: 0.09791 / Net I/σ(I): 33.73
Reflection shellResolution: 2.189→2.267 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.5983 / Mean I/σ(I) obs: 7.03 / Num. unique obs: 7178 / CC1/2: 0.954 / Rrim(I) all: 0.6245 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NVB

2nvb


Resolution: 2.189→47.098 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.75
RfactorNum. reflection% reflection
Rfree0.2537 2006 2.73 %
Rwork0.2051 --
obs0.2064 73407 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.189→47.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10535 0 10 107 10652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810721
X-RAY DIFFRACTIONf_angle_d0.87114516
X-RAY DIFFRACTIONf_dihedral_angle_d13.7236412
X-RAY DIFFRACTIONf_chiral_restr0.0581702
X-RAY DIFFRACTIONf_plane_restr0.0061833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1888-2.24350.30731490.23864896X-RAY DIFFRACTION97
2.2435-2.30420.26671350.23015031X-RAY DIFFRACTION99
2.3042-2.3720.30141360.2225043X-RAY DIFFRACTION99
2.372-2.44850.2811430.22825056X-RAY DIFFRACTION100
2.4485-2.5360.30081340.22745038X-RAY DIFFRACTION99
2.536-2.63760.2851510.23425052X-RAY DIFFRACTION100
2.6376-2.75760.32691450.23335099X-RAY DIFFRACTION100
2.7576-2.9030.31541400.24365068X-RAY DIFFRACTION100
2.903-3.08480.26061380.23665123X-RAY DIFFRACTION100
3.0848-3.32290.3011470.23255118X-RAY DIFFRACTION100
3.3229-3.65720.27251490.20865140X-RAY DIFFRACTION100
3.6572-4.18620.22411440.18385162X-RAY DIFFRACTION100
4.1862-5.2730.21451450.16295203X-RAY DIFFRACTION100
5.273-47.10920.20071500.18675372X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.4486 Å / Origin y: -4.6939 Å / Origin z: -6.6952 Å
111213212223313233
T0.2849 Å2-0.0043 Å20.0016 Å2-0.254 Å20.0029 Å2--0.3053 Å2
L0.4641 °2-0.0682 °2-0.0888 °2-0.5848 °2-0.0197 °2--0.3971 °2
S0.033 Å °-0.0218 Å °0.0065 Å °0.0376 Å °-0.0357 Å °-0.0981 Å °-0.0273 Å °0.0125 Å °0.0004 Å °
Refinement TLS groupSelection details: all

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