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Basic information

Entry
Database: PDB / ID: 4uwq
TitleCrystal structure of the disulfide-linked complex of the thiosulfodyrolase SoxB with the carrier-protein SoxYZ from Thermus thermophilus
Components
  • SOXY PROTEIN
  • SOXZ
  • SULFUR OXIDATION PROTEIN SOXB
KeywordsHYDROLASE
Function / homology
Function and homology information


nucleotide catabolic process / outer membrane-bounded periplasmic space / hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Helix Hairpins - #570 / Sulphur oxidation protein SoxZ / Thiosulfate oxidation carrier complex protein SoxZ / Thiosulfohydrolase SoxB / SoxB, N-terminal metallophosphatase domain / Sulphur oxidation protein SoxZ / SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily ...Helix Hairpins - #570 / Sulphur oxidation protein SoxZ / Thiosulfate oxidation carrier complex protein SoxZ / Thiosulfohydrolase SoxB / SoxB, N-terminal metallophosphatase domain / Sulphur oxidation protein SoxZ / SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily / Sulfur oxidation protein SoxY / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Helix Hairpins / Metallo-dependent phosphatase-like / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Helix non-globular / Special / 4-Layer Sandwich / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / SoxY protein / SoxZ / Sulfur oxidation protein soxB
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsGrabarczyk, D.B. / Chappell, P.E. / Johnson, S. / Stelzl, L.S. / Lea, S.M. / Berks, B.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural Basis for Specificity and Promiscuity in a Carrier Protein/Enzyme System from the Sulfur Cycle
Authors: Grabarczyk, D.B. / Chappell, P.E. / Johnson, S. / Stelzl, L.S. / Lea, S.M. / Berks, B.C.
History
DepositionAug 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Dec 14, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFUR OXIDATION PROTEIN SOXB
B: SOXY PROTEIN
C: SOXZ
D: SULFUR OXIDATION PROTEIN SOXB
E: SOXY PROTEIN
F: SOXZ
G: SULFUR OXIDATION PROTEIN SOXB
H: SOXY PROTEIN
I: SOXZ
J: SULFUR OXIDATION PROTEIN SOXB
K: SOXY PROTEIN
L: SOXZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,43020
Polymers356,99112
Non-polymers4408
Water19811
1
J: SULFUR OXIDATION PROTEIN SOXB
K: SOXY PROTEIN
L: SOXZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3585
Polymers89,2483
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-33.8 kcal/mol
Surface area30380 Å2
MethodPISA
2
D: SULFUR OXIDATION PROTEIN SOXB
E: SOXY PROTEIN
F: SOXZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3585
Polymers89,2483
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-22.9 kcal/mol
Surface area30200 Å2
MethodPISA
3
A: SULFUR OXIDATION PROTEIN SOXB
B: SOXY PROTEIN
C: SOXZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3585
Polymers89,2483
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-29.7 kcal/mol
Surface area30100 Å2
MethodPISA
4
G: SULFUR OXIDATION PROTEIN SOXB
H: SOXY PROTEIN
I: SOXZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3585
Polymers89,2483
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-20.2 kcal/mol
Surface area36350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.220, 115.950, 120.940
Angle α, β, γ (deg.)86.51, 83.21, 89.77
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.199, -0.978, -0.061), (0.976, 0.203, -0.078), (0.089, -0.044, 0.995)1.65533, 0.86659, 0.20506
2given(1, 0.009, -0.013), (0.01, -1, 0.024), (-0.013, -0.024, -1)-0.58604, 1.74781, 0.31152
3given(0.214, -0.973, -0.086), (-0.974, -0.22, 0.057), (-0.075, 0.072, -0.995)1.18061, 0.89887, 0.07123
4given(0.133, -0.988, -0.083), (0.991, 0.132, 0.015), (-0.004, -0.084, 0.996)1.68754, 0.87793, 0.24452
5given(1, -0.018, -0.005), (-0.018, -1, 0.01), (-0.006, -0.01, -1)-0.55778, 1.75874, 0.30257
6given(0.139, -0.985, -0.099), (-0.99, -0.139, -0.014), (0.1, -0.995)1.22648, 0.87482, 0.0422
7given(0.111, -0.989, -0.102), (0.994, 0.109, 0.02), (-0.008, -0.104, 0.995)1.7093, 0.88439, 0.25645
8given(0.999, -0.044, 0.016), (-0.044, -0.999, -0.009), (0.016, 0.009, -1)-0.54075, 1.77286, 0.29057
9given(0.107, -0.984, -0.145), (-0.994, -0.105, -0.02), (0.005, 0.147, -0.989)1.2752, 0.86708, 0.01534

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Components

#1: Protein
SULFUR OXIDATION PROTEIN SOXB / SOXB


Mass: 62664.371 Da / Num. of mol.: 4 / Fragment: RESIDUES 23-573 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS HB27 (bacteria) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): STAR / References: UniProt: Q72IT0
#2: Protein
SOXY PROTEIN / SOXY


Mass: 14718.761 Da / Num. of mol.: 4 / Fragment: RESIDUES 29-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS HB27 (bacteria) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): STAR / References: UniProt: Q72IS6
#3: Protein
SOXZ


Mass: 11864.509 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS HB27 (bacteria) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): STAR / References: UniProt: Q72IS7
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.18 % / Description: NONE
Crystal growpH: 8.3
Details: 0.1M TRIS-HCL, 0.2M (NH4)2SO4, 8.55% PEG 8000, PH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9999
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.28→59.81 Å / Num. obs: 112492 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 90.37 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9
Reflection shellResolution: 3.28→3.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSTHROUGH XIA2data reduction
AimlessTHROUGH XIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2WDF, 1V8H AND AN UNPUBLISHED SOXY STRUCTURE

2wdf

1v8h


Resolution: 3.28→59.81 Å / Cor.coef. Fo:Fc: 0.8229 / Cor.coef. Fo:Fc free: 0.827 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.543
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=23073. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=23073. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 2894 5.07 %RANDOM
Rwork0.2693 ---
obs0.2696 57113 98.52 %-
Displacement parametersBiso mean: 92.77 Å2
Baniso -1Baniso -2Baniso -3
1--24.3031 Å28.1134 Å21.4763 Å2
2--0.3326 Å26.0785 Å2
3---23.9704 Å2
Refine analyzeLuzzati coordinate error obs: 0.855 Å
Refinement stepCycle: LAST / Resolution: 3.28→59.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23062 0 8 11 23081
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00723615HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8432099HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7949SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes508HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3474HARMONIC5
X-RAY DIFFRACTIONt_it23615HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.48
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2950SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24556SEMIHARMONIC4
LS refinement shellResolution: 3.28→3.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3004 232 5.62 %
Rwork0.2762 3898 -
all0.2776 4130 -
obs--98.52 %

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