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- PDB-4v4d: Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase f... -

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Basic information

Entry
Database: PDB / ID: 4v4d
TitleCrystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with pyrogallol
Components(Pyrogallol hydroxytransferase ...) x 2
KeywordsOXIDOREDUCTASE / Molybdenum binding enzyme / MGD-cofactors / DMSO-reductase family / 4Fe-4S-cluster / complex with substrate pyrogallol
Function / homology
Function and homology information


pyrogallol hydroxytransferase / pyrogallol hydroxytransferase activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
: / Pyrogallol hydroxytransferase large subunit-like, domain 1 / : / : / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase ...: / Pyrogallol hydroxytransferase large subunit-like, domain 1 / : / : / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Immunoglobulin-like fold
Similarity search - Domain/homology
MOLYBDENUM(IV) ION / Chem-MGD / BENZENE-1,2,3-TRIOL / IRON/SULFUR CLUSTER / Pyrogallol hydroxytransferase large subunit / Pyrogallol hydroxytransferase small subunit
Similarity search - Component
Biological speciesPelobacter acidigallici (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMesserschmidt, A. / Niessen, H. / Abt, D. / Einsle, O. / Schink, B. / Kroneck, P.M.H.
CitationJournal: PROC.NATL.ACAD.SCI.USA / Year: 2004
Title: Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols
Authors: Messerschmidt, A. / Niessen, H. / Abt, D. / Einsle, O. / Schink, B. / Kroneck, P.M.H.
History
DepositionJun 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1VLE, 1TI4
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details
Remark 400THE COMPLETE CRYSTAL STRUCTURE IS REPRESENTED BY PDB STRUCTURES 1TI4 AND 1VLE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrogallol hydroxytransferase large subunit
B: Pyrogallol hydroxytransferase small subunit
C: Pyrogallol hydroxytransferase large subunit
D: Pyrogallol hydroxytransferase small subunit
E: Pyrogallol hydroxytransferase large subunit
F: Pyrogallol hydroxytransferase small subunit
G: Pyrogallol hydroxytransferase large subunit
H: Pyrogallol hydroxytransferase small subunit
I: Pyrogallol hydroxytransferase large subunit
J: Pyrogallol hydroxytransferase small subunit
K: Pyrogallol hydroxytransferase large subunit
L: Pyrogallol hydroxytransferase small subunit
M: Pyrogallol hydroxytransferase large subunit
N: Pyrogallol hydroxytransferase small subunit
O: Pyrogallol hydroxytransferase large subunit
P: Pyrogallol hydroxytransferase small subunit
Q: Pyrogallol hydroxytransferase large subunit
R: Pyrogallol hydroxytransferase small subunit
S: Pyrogallol hydroxytransferase large subunit
T: Pyrogallol hydroxytransferase small subunit
U: Pyrogallol hydroxytransferase large subunit
V: Pyrogallol hydroxytransferase small subunit
W: Pyrogallol hydroxytransferase large subunit
X: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,601,691131
Polymers1,567,67224
Non-polymers34,019107
Water181,75310089
1
A: Pyrogallol hydroxytransferase large subunit
B: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Pyrogallol hydroxytransferase large subunit
D: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Pyrogallol hydroxytransferase large subunit
F: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Pyrogallol hydroxytransferase large subunit
H: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Pyrogallol hydroxytransferase large subunit
J: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,43710
Polymers130,6392
Non-polymers2,7988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Pyrogallol hydroxytransferase large subunit
L: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Pyrogallol hydroxytransferase large subunit
N: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Pyrogallol hydroxytransferase large subunit
P: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q: Pyrogallol hydroxytransferase large subunit
R: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: Pyrogallol hydroxytransferase large subunit
T: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Pyrogallol hydroxytransferase large subunit
V: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
W: Pyrogallol hydroxytransferase large subunit
X: Pyrogallol hydroxytransferase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47811
Polymers130,6392
Non-polymers2,8389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.473, 178.140, 179.050
Angle α, β, γ (deg.)64.11, 64.45, 65.11
Int Tables number1
Space group name H-MP1

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Components

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Pyrogallol hydroxytransferase ... , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein
Pyrogallol hydroxytransferase large subunit / Transhydroxylase alpha subunit


Mass: 99379.898 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pelobacter acidigallici (bacteria) / Strain: MaGal 2(DSM 2377) / References: UniProt: P80563, pyrogallol hydroxytransferase
#2: Protein
Pyrogallol hydroxytransferase small subunit / Transhydroxylase beta subunit


Mass: 31259.424 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pelobacter acidigallici (bacteria) / Strain: MaGal 2(DSM 2377) / References: UniProt: P80564, pyrogallol hydroxytransferase

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Non-polymers , 6 types, 10196 molecules

#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical
ChemComp-4MO / MOLYBDENUM(IV) ION


Mass: 95.940 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mo
#6: Chemical
ChemComp-PYG / BENZENE-1,2,3-TRIOL / PYROGALLOL


Mass: 126.110 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H6O3
#7: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Fe4S4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10089 / 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: 2.71 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, sodium acetate, potassium phosphate, sodium dithionite, sodium cacodylate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2002 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 840476 / Num. obs: 814421 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 5.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.515 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1TI2

1ti2
PDB Unreleased entry


Resolution: 2.2→24.99 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 4990834.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 81375 10 %RANDOM
Rwork0.178 ---
obs0.178 814421 96.7 %-
all-842214 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5217 Å2 / ksol: 0.381544 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.27 Å2-0.88 Å2
2--0.05 Å2-0.03 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55080 0 779 5061 60920
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d2.54
X-RAY DIFFRACTIONc_mcbond_it1.912.5
X-RAY DIFFRACTIONc_mcangle_it2.583.5
X-RAY DIFFRACTIONc_scbond_it3.553.5
X-RAY DIFFRACTIONc_scangle_it4.54.9
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.002 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 13167 9.8 %
Rwork0.228 121399 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SPECIAL_GROUPS_NEW.PARSPECIAL_GROUPS_TH_HH.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4PYR_TH_HH_ACT_1.PARPYR_TH_HH_ACT_1.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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