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- PDB-6rxd: Crystal Structure of Bifidobacterium longum Multiple Inositol Pol... -

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Basic information

Entry
Database: PDB / ID: 6rxd
TitleCrystal Structure of Bifidobacterium longum Multiple Inositol Polyphosphate Phosphatase Apo Form
ComponentsHistidine acid phosphatase
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Bifidobacterium
Function / homologyHistidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / hydrolase activity / membrane / metal ion binding / Histidine acid phosphatase
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLi, A.W.H. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022978/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Snapshots during the catalytic cycle of a histidine acid phytase reveal an induced-fit structural mechanism.
Authors: Acquistapace, I.M. / Zi Etek, M.A. / Li, A.W.H. / Salmon, M. / Kuhn, I. / Bedford, M.R. / Brearley, C.A. / Hemmings, A.M.
History
DepositionJun 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine acid phosphatase
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4186
Polymers112,1562
Non-polymers2624
Water23,1851287
1
A: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2093
Polymers56,0781
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2093
Polymers56,0781
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.660, 72.940, 88.160
Angle α, β, γ (deg.)71.61, 72.10, 77.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Histidine acid phosphatase


Mass: 56078.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_0263 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1287 / 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: 2.8 Å3/Da / Density % sol: 56.11 % / Description: Needle
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 0.01 M zinc chloride, 18 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2013
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→46.53 Å / Num. obs: 141139 / % possible obs: 95.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.7
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6851 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDT

4fdt


Resolution: 1.65→46.528 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.76
RfactorNum. reflection% reflection
Rfree0.1771 7078 5.02 %
Rwork0.1532 --
obs0.1544 141114 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→46.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7812 0 4 1287 9103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068263
X-RAY DIFFRACTIONf_angle_d1.00811253
X-RAY DIFFRACTIONf_dihedral_angle_d13.7593083
X-RAY DIFFRACTIONf_chiral_restr0.0731164
X-RAY DIFFRACTIONf_plane_restr0.0051526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66880.24852190.23384395X-RAY DIFFRACTION95
1.6688-1.68840.27782260.2254358X-RAY DIFFRACTION95
1.6884-1.7090.2252230.2184445X-RAY DIFFRACTION95
1.709-1.73060.24842240.20864496X-RAY DIFFRACTION96
1.7306-1.75340.26522400.2134391X-RAY DIFFRACTION96
1.7534-1.77740.25742340.20514428X-RAY DIFFRACTION95
1.7774-1.80280.23162140.18884473X-RAY DIFFRACTION95
1.8028-1.82970.20032170.18454464X-RAY DIFFRACTION96
1.8297-1.85830.20862400.1734412X-RAY DIFFRACTION96
1.8583-1.88880.21592490.18534450X-RAY DIFFRACTION96
1.8888-1.92130.22922380.19334424X-RAY DIFFRACTION95
1.9213-1.95630.20372380.17654441X-RAY DIFFRACTION96
1.9563-1.99390.19672390.16864356X-RAY DIFFRACTION96
1.9939-2.03460.20392500.1614512X-RAY DIFFRACTION96
2.0346-2.07880.19642320.16164466X-RAY DIFFRACTION96
2.0788-2.12720.18112420.15424489X-RAY DIFFRACTION97
2.1272-2.18040.17622220.15094483X-RAY DIFFRACTION96
2.1804-2.23930.17762600.14654418X-RAY DIFFRACTION97
2.2393-2.30520.19882540.15184484X-RAY DIFFRACTION96
2.3052-2.37960.17792410.14474545X-RAY DIFFRACTION97
2.3796-2.46470.16482040.14474498X-RAY DIFFRACTION97
2.4647-2.56340.18962380.14374501X-RAY DIFFRACTION97
2.5634-2.680.16852530.14644556X-RAY DIFFRACTION98
2.68-2.82130.16752730.14394482X-RAY DIFFRACTION98
2.8213-2.9980.1762250.15214535X-RAY DIFFRACTION98
2.998-3.22950.19142470.15094515X-RAY DIFFRACTION97
3.2295-3.55430.15432330.14024484X-RAY DIFFRACTION97
3.5543-4.06840.14072590.13024499X-RAY DIFFRACTION98
4.0684-5.12470.12752190.12344507X-RAY DIFFRACTION97
5.1247-46.5470.16382250.15714529X-RAY DIFFRACTION97
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)
10.52480.2236-0.3360.3212-0.15440.4471-0.09080.1542-0.0678-0.05550.0643-0.01280.0474-0.1495-0.0070.0935-0.0063-0.01450.131-0.0050.0979-3.9047-1.1536-4.7679
20.39060.0876-0.21140.2422-0.10.1538-0.0262-0.0649-0.13110.03440.0623-0.00430.08030.022-00.12040.0229-0.00120.12180.02450.1451-14.956-11.597518.7337
30.35960.2222-0.28150.306-0.07520.275-0.0150.0311-0.0203-0.0020.0162-0.0222-0.0121-0.0410.00060.08910.0156-0.01450.1107-0.00250.11922.20551.38834.812
40.24420.1280.02480.24760.0670.3584-0.07660.0271-0.1023-0.06350.0467-0.0986-0.08060.0526-0.00240.1135-0.01380.00410.13080.00660.126818.840713.1045-12.8833
50.12670.0085-0.3290.4793-0.01250.55760.0182-0.00520.0787-0.02240.052-0.06450.0458-0.07280.08430.10860.0015-0.00350.1130.00410.13429.989435.506412.6173
60.14980.1343-0.30580.5482-0.13580.45690.1032-0.02130.06580.0982-0.0079-0.005-0.12490.06350.0150.1389-0.0058-0.02030.1335-0.01440.11418.931534.622526.155
70.31430.0939-0.26340.40630.00550.54070.031-0.17240.28290.12110.1823-0.19210.0690.09140.34440.12820.0359-0.02750.1476-0.0860.234222.235340.10389.5123
80.2761-0.0333-0.31930.34650.2670.50290.0039-0.0202-0.04740.1315-0.03370.01840.04950.0133-0.00170.1598-0.0111-0.00320.11220.00390.10473.987519.149329.7104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 234 )
2X-RAY DIFFRACTION2chain 'A' and (resid 235 through 300 )
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 444 )
4X-RAY DIFFRACTION4chain 'A' and (resid 445 through 515 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 95 )
6X-RAY DIFFRACTION6chain 'B' and (resid 96 through 258 )
7X-RAY DIFFRACTION7chain 'B' and (resid 259 through 335 )
8X-RAY DIFFRACTION8chain 'B' and (resid 336 through 515 )

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