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- PDB-6nlr: Crystal structure of the putative histidinol phosphatase hisK fro... -

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Entry
Database: PDB / ID: 6nlr
TitleCrystal structure of the putative histidinol phosphatase hisK from Listeria monocytogenes with trinuclear metals determined by PIXE revealing sulphate ion in active site. Based on PIXE analysis and original date from 3DCP
ComponentsHistidinol-phosphatase
KeywordsHYDROLASE / HISTIDINOL PHOSPHATASE / HISK / HISTIDINE BIOSYNTHESIS / NESG / LMR14 / PIXE / TRINUCLEAR / SULPHATE
Function / homologyMetal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : / : / : / :
Function and homology information
Biological speciesListeria monocytogenes serotype 4b str. H7858 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSnell, E.H. / Garman, E.F. / Lowe, E.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application.
Authors: Grime, G.W. / Zeldin, O.B. / Snell, M.E. / Lowe, E.D. / Hunt, J.F. / Montelione, G.T. / Tong, L. / Snell, E.H. / Garman, E.F.
History
DepositionJan 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Remark 0THIS ENTRY 6NLR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3DCP, DETERMINED BY S.M. ...THIS ENTRY 6NLR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3DCP, DETERMINED BY S.M.VOROBIEV,M.SU,J.SEETHARAMAN,L.ZHAO,L.MAO,E.L.FOOTE,R.XIAO,R.NAIR,M.C.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidinol-phosphatase
B: Histidinol-phosphatase
C: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,42017
Polymers98,5433
Non-polymers87714
Water9,530529
1
A: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1125
Polymers32,8481
Non-polymers2654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1546
Polymers32,8481
Non-polymers3075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histidinol-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1536
Polymers32,8481
Non-polymers3065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.278, 191.278, 48.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA1 - 2721 - 272
21TYRTYRBB1 - 2721 - 272
12CYSCYSAA1 - 2731 - 273
22CYSCYSCC1 - 2731 - 273
13TYRTYRBB1 - 2721 - 272
23TYRTYRCC1 - 2721 - 272

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Histidinol-phosphatase


Mass: 32847.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serotype 4b str. H7858 (bacteria)
Gene: hisk, DYZ35_00104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) + MAGIC / References: UniProt: A0A3A6YEN9, histidinol-phosphatase

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Non-polymers , 6 types, 543 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.23 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3DCP.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 15% PEG 8000, 0.17 M SODIUM ACETATE, 0.01 M L-CYSTEINE, 0.1 M MES PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2008 / Details: FLAT COLLIMATING MIRROR, TOROID, FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1→41.6 Å / Num. obs: 114574 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 23.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 12134 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→41.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.658 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18583 2868 4.9 %RANDOM
Rwork0.15488 ---
obs0.15638 55392 98.4 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å2-0 Å2
2--0.1 Å20 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 2.1→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 26 529 7175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136816
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176042
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6499187
X-RAY DIFFRACTIONr_angle_other_deg1.3411.57814091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87523.767377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1441524
X-RAY DIFFRACTIONr_chiral_restr0.070.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021475
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_it1.9831.9753303
X-RAY DIFFRACTIONr_mcbond_other1.9791.9733302
X-RAY DIFFRACTIONr_mcangle_it2.7142.9484127
X-RAY DIFFRACTIONr_mcangle_other2.7152.9494128
X-RAY DIFFRACTIONr_scbond_it3.5852.3443513
X-RAY DIFFRACTIONr_scbond_other3.4832.3333499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9633.3675042
X-RAY DIFFRACTIONr_long_range_B_refined6.48524.5837755
X-RAY DIFFRACTIONr_long_range_B_other6.42324.4357716
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)
11A91820.07
12B91820.07
21A92000.07
22C92000.07
31B93100.06
32C93100.06
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 199 -
Rwork0.208 3896 -
obs--95.32 %
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)
11.025-0.2082-0.22291.61940.50361.18420.01660.0428-0.0518-0.03450.017-0.07290.0581-0.038-0.03370.0342-0.0334-0.00170.04940.01510.0309-60.30668.6941.142
22.35610.49-1.19381.0922-0.18541.59010.11240.12920.1173-0.04550.0199-0.0222-0.1842-0.0357-0.13240.07060.03340.03820.06080.01410.0831-31.39121.39341.096
31.08860.4632-0.011.50250.48351.93430.062-0.00340.01390.03460.039-0.0464-0.04090.1026-0.10110.0337-0.01160.02640.0231-0.00060.0374-66.22331.41357.278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 277
2X-RAY DIFFRACTION2B1 - 273
3X-RAY DIFFRACTION3C1 - 274

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