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- PDB-4mdz: Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodies... -

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Basic information

Entry
Database: PDB / ID: 4mdz
TitleCrystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre
ComponentsMetal dependent phosphohydrolase
KeywordsHYDROLASE / Structural Genomics / Oxford Protein Production Facility / OPPF / phosphohydrolase
Function / homology
Function and homology information


hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / HD-GYP domain / HD domain / HD-GYP domain profile. / HDIG domain / Hypothetical protein af1432 / Hypothetical protein af1432 / GAF domain / HD domain / GAF domain ...: / HD-GYP domain / HD domain / HD-GYP domain profile. / HDIG domain / Hypothetical protein af1432 / Hypothetical protein af1432 / GAF domain / HD domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta-Lactamase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / : / SUCCINIC ACID / Metal dependent phosphohydrolase
Similarity search - Component
Biological speciesPersephonella marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsBellini, D. / Walsh, M.A. / Oxford Protein Production Facility (OPPF)
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre.
Authors: Bellini, D. / Caly, D.L. / McCarthy, Y. / Bumann, M. / An, S.Q. / Dow, J.M. / Ryan, R.P. / Walsh, M.A.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.title / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Metal dependent phosphohydrolase
B: Metal dependent phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,03612
Polymers85,5322
Non-polymers1,50410
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-82 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.190, 183.010, 233.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-544-

HOH

Detailsasymmetric unit contains one dimer, which is the biological assembly

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Components

#1: Protein Metal dependent phosphohydrolase


Mass: 42765.781 Da / Num. of mol.: 2 / Mutation: C41A, C197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persephonella marina (bacteria) / Strain: DSM 14350 / EX-H1 / Gene: PERMA_0986 / Production host: Escherichia coli (E. coli) / References: UniProt: C0QQ26
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.9 M succinate pH 7, 2% PEG 2000, 0.1 M MES buffer pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 18, 2013 / Details: mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.68→66 Å / Num. all: 44989 / Num. obs: 42290 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.3
Reflection shellResolution: 2.68→2.75 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
EDNAdata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MCW

4mcw


Resolution: 2.68→65.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 21.081 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 2107 5 %RANDOM
Rwork0.18369 ---
all0.186 42290 --
obs0.18594 40177 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.842 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å2-0 Å2
2--3.14 Å2-0 Å2
3----1.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.243 Å0.314 Å
Luzzati sigma a-0.193 Å
Refinement stepCycle: LAST / Resolution: 2.68→65.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5929 0 90 96 6115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026135
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9848272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46723.792298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.317151149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.721548
X-RAY DIFFRACTIONr_chiral_restr0.1120.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214588
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 124 -
Rwork0.357 2756 -
obs-2756 99.28 %
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)
12.4448-0.4613-0.2371.87610.53182.2591-0.0380.28850.1469-0.2422-0.04650.0501-0.165-0.0770.08440.1191-0.002-0.00220.0795-0.04110.1134-2.81247.98454.291
21.39140.14210.09390.72310.31761.75860.001-0.10420.0550.02260.0410.060.1432-0.0901-0.0420.0838-0.00050.00110.13290.00260.0737-1.62521.21517.659
31.61710.03070.10933.003-0.17112.0615-0.08470.0501-0.20430.17530.0219-0.26640.41460.04170.06280.2386-0.02050.07850.0136-0.04070.15545.89617.36563.691
41.73830.47030.48491.05390.15931.2106-0.01750.2007-0.0539-0.04050.0676-0.12730.03860.2816-0.050.05360.0040.01480.2404-0.05930.121527.81631.9624.616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 159
2X-RAY DIFFRACTION2A160 - 360
3X-RAY DIFFRACTION3B-2 - 159
4X-RAY DIFFRACTION4B160 - 360

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