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- PDB-4ras: Reductive dehalogenase structure suggests a mechanism for B12-dep... -

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Basic information

Entry
Database: PDB / ID: 4ras
TitleReductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation
ComponentsOxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
KeywordsOXIDOREDUCTASE / ferrodoxin and cobalamin-binding domain / Reductive dehalogenase / iron sulfur binding / cobalamin binding
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / metal ion binding / plasma membrane
Similarity search - Function
Reductive dehalogenase domain / Reductive dehalogenase subunit / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
COBALAMIN / IRON/SULFUR CLUSTER / Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
Similarity search - Component
Biological speciesNitratireductor pacificus pht-3B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsQuezada, C.P. / Payne, K.A.P. / Leys, D.
CitationJournal: Nature / Year: 2015
Title: Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation.
Authors: Payne, K.A. / Quezada, C.P. / Fisher, K. / Dunstan, M.S. / Collins, F.A. / Sjuts, H. / Levy, C. / Hay, S. / Rigby, S.E. / Leys, D.
History
DepositionSep 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
B: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
C: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,57618
Polymers232,2993
Non-polymers6,27615
Water5,062281
1
A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5256
Polymers77,4331
Non-polymers2,0925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5256
Polymers77,4331
Non-polymers2,0925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5256
Polymers77,4331
Non-polymers2,0925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
C: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,05012
Polymers154,8662
Non-polymers4,18410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-177 kcal/mol
Surface area48610 Å2
MethodPISA
5
A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules

A: Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,05012
Polymers154,8662
Non-polymers4,18410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Buried area8530 Å2
ΔGint-176 kcal/mol
Surface area48880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.340, 171.510, 109.020
Angle α, β, γ (deg.)90.00, 98.87, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA1 - 6971 - 697
21ALAALABB1 - 6971 - 697
12SERSERAA1 - 6961 - 696
22SERSERCC1 - 6961 - 696
13SERSERBB1 - 6961 - 696
23SERSERCC1 - 6961 - 696

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein / / Reductive dehalogenase


Mass: 77433.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratireductor pacificus pht-3B (bacteria)
Gene: NA2_14372 / Production host: Bacillus megaterium (bacteria) / References: UniProt: K2MB66

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Non-polymers , 5 types, 296 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.53 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M potassium thiocyanate, 0.1M sodium cacodylate, 8% PEG 20K 8 % PEG 550 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→76.9 Å / Num. all: 133721 / Num. obs: 133721 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 34001 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata scaling
MLPHAREphasing
REFMAC5.7.0029refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→76.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 12.413 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20658 6966 5 %RANDOM
Rwork0.18119 ---
all0.18244 133721 --
obs0.18244 133721 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.118 Å2
Baniso -1Baniso -2Baniso -3
1-4.01 Å20 Å2-1.38 Å2
2--0.79 Å20 Å2
3----4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→76.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15828 0 327 281 16436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01916572
X-RAY DIFFRACTIONr_bond_other_d0.0080.0215618
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.99622772
X-RAY DIFFRACTIONr_angle_other_deg1.636335826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47152075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41822.596728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.071152624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.06215180
X-RAY DIFFRACTIONr_chiral_restr0.1110.22399
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02119185
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023769
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A428800.02
12B428800.02
21A424090.03
22C424090.03
31B420670.03
32C420670.03
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 510 -
Rwork0.312 9993 -
obs--99.63 %
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)
10.42850.19120.14460.1770.09560.7051-0.02770.0175-0.0337-0.0560.029-0.0259-0.09980.0314-0.00130.3372-0.02440.06250.0064-0.00850.2476156.87741.955135.071
20.2365-0.37160.25210.8188-0.2940.5774-0.0228-0.0066-0.03450.0740.06540.0401-0.01530.0127-0.04260.37130.13530.05080.12830.02390.2773200.3980.049114.123
30.4535-0.1388-0.05461.1589-0.29980.9782-0.1143-0.12830.01870.2160.04950.0456-0.2330.08210.06470.59430.2520.01060.2532-0.00270.3116195.6475.614167.588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 698
2X-RAY DIFFRACTION1A801 - 803
3X-RAY DIFFRACTION2B1 - 697
4X-RAY DIFFRACTION2B801 - 803
5X-RAY DIFFRACTION3C1 - 696
6X-RAY DIFFRACTION3C801 - 803

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