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- PDB-9gof: MncA bound to nickel -

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Basic information

Entry
Database: PDB / ID: 9gof
TitleMncA bound to nickel
ComponentsSll1358 protein
KeywordsMETAL BINDING PROTEIN / Metalloenzyme
Function / homology
Function and homology information


oxalate metabolic process / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bicupin, oxalate decarboxylase/oxidase / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
ACETIC ACID / GLYCINE / NICKEL (II) ION / Sll1358 protein
Similarity search - Component
Biological speciesSynechocystis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGlasfeld, A. / Robinson, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: A metal-trap tests and refines blueprints to engineer cellular protein metalation with different elements.
Authors: Clough, S.E. / Young, T.R. / Tarrant, E. / Scott, A.J.P. / Chivers, P.T. / Glasfeld, A. / Robinson, N.J.
History
DepositionSep 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sll1358 protein
B: Sll1358 protein
C: Sll1358 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,48715
Polymers118,5523
Non-polymers93612
Water17,060947
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, confirmed by mass photometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17030 Å2
ΔGint-163 kcal/mol
Surface area36570 Å2
Unit cell
Length a, b, c (Å)235.185, 235.185, 132.008
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11B-1412-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Sll1358 protein


Mass: 39517.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Signal sequence from native gene is deleted (residues 2-34)
Source: (gene. exp.) Synechocystis (bacteria) / Gene: sll1358 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P73510

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Non-polymers , 5 types, 959 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 947 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 10% PEG 8000, 0.1 M sodium acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→80.63 Å / Num. obs: 280693 / % possible obs: 99.9 % / Redundancy: 158 % / Biso Wilson estimate: 22.24 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.267 / Net I/σ(I): 16.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 100 % / Mean I/σ(I) obs: 0.54 / Num. unique obs: 15191 / CC1/2: 0.63 / Rpim(I) all: 0.44 / Rrim(I) all: 4.58 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→80.63 Å / SU ML: 0.2294 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1766 14062 5.06 %
Rwork0.1636 263916 -
obs0.1642 277978 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.81 Å2
Refinement stepCycle: LAST / Resolution: 1.6→80.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8242 0 45 947 9234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00648598
X-RAY DIFFRACTIONf_angle_d0.867211744
X-RAY DIFFRACTIONf_chiral_restr0.05981261
X-RAY DIFFRACTIONf_plane_restr0.00781520
X-RAY DIFFRACTIONf_dihedral_angle_d8.44741156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.42044430.41998521X-RAY DIFFRACTION97.81
1.62-1.640.41524600.38948647X-RAY DIFFRACTION99.12
1.64-1.660.36134430.3388685X-RAY DIFFRACTION99.13
1.66-1.680.31434650.29958681X-RAY DIFFRACTION99.8
1.68-1.70.2825020.27258698X-RAY DIFFRACTION99.98
1.7-1.720.26034760.24138695X-RAY DIFFRACTION99.97
1.72-1.750.22624440.21488763X-RAY DIFFRACTION100
1.75-1.770.20734910.1978718X-RAY DIFFRACTION99.96
1.77-1.80.20984720.18118720X-RAY DIFFRACTION99.98
1.8-1.830.1964760.16358739X-RAY DIFFRACTION99.99
1.83-1.860.17544740.16418748X-RAY DIFFRACTION100
1.86-1.90.17394270.16058784X-RAY DIFFRACTION100
1.9-1.930.19094870.16838711X-RAY DIFFRACTION100
1.93-1.970.1764340.17388815X-RAY DIFFRACTION99.99
1.97-2.020.2024500.17978761X-RAY DIFFRACTION99.98
2.02-2.060.17084690.15758778X-RAY DIFFRACTION99.99
2.06-2.110.17174790.14858736X-RAY DIFFRACTION99.98
2.11-2.170.16144670.14878805X-RAY DIFFRACTION100
2.17-2.240.15634560.15088795X-RAY DIFFRACTION99.98
2.24-2.310.18384530.15678805X-RAY DIFFRACTION100
2.31-2.390.17034820.15388794X-RAY DIFFRACTION100
2.39-2.490.17564730.15778803X-RAY DIFFRACTION100
2.49-2.60.17864670.16258829X-RAY DIFFRACTION99.99
2.6-2.740.19684880.16688834X-RAY DIFFRACTION100
2.74-2.910.17654530.16318878X-RAY DIFFRACTION100
2.91-3.130.17554910.16248875X-RAY DIFFRACTION100
3.13-3.450.16254980.15848880X-RAY DIFFRACTION100
3.45-3.950.16994720.15028968X-RAY DIFFRACTION100
3.95-4.970.12684630.11989065X-RAY DIFFRACTION99.99
4.97-80.630.14325070.14969385X-RAY DIFFRACTION99.78
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)
13.06275592521-0.943669820391-0.1365499804170.888030735734-0.01370377899790.3437031489210.03629340922030.09384596849980.244501431697-0.00864235830246-0.0412431595232-0.0846056587127-0.06952583386450.05294819349910.01141053119870.226992478512-0.03865418760690.0005462142813160.1833203210090.01131608905060.22956591915294.8730143349-9.731011812367.38847076213
22.159979064150.21822015820.2223634836040.693004988755-0.2394837475021.46003484670.0528770046639-0.1411875542550.08713493699490.0837204689822-0.04475749362360.0161812339482-0.04707435745790.00934046658808-0.005950833579340.191995060026-0.01340938241180.006307668382190.148934843252-0.01086497645410.21063912818973.6284871167-15.626872735814.250750094
30.598844719778-0.2387682250240.2575776700990.44346261064-0.1092561622640.4839500226290.0307492199722-0.03179949146460.04679722077050.00256447347359-0.01887376796270.0665049345577-0.0431590064074-0.0052513394722-0.01559898277390.210604439414-0.01606916534580.009178675648590.171555788998-0.006776825003580.24501486410968.6032660793-15.49610950049.93338688777
41.22099315307-0.3203910721470.04636841411140.178954364941-0.1093115498360.1945678253270.0179144624649-0.1046168210010.1504990951380.0499672678797-0.00700126484035-0.0168648459179-0.0504090819410.0682634313499-0.01264252394730.20754991511-0.0317947365933-0.008573598197620.212385016424-0.01007329505310.21620041139398.049282498-20.773027872216.3432747595
51.19799387127-0.9802931178890.005485586743760.629146466666-0.245332193170.0375085525423-0.0481370722346-0.1308815941290.08991967739470.09483322912510.0284712291666-0.0590508586755-0.05198417066670.0911043116196-0.01080678716340.231008272736-0.0288223074537-0.03415494054210.291202068098-0.005185826364330.228533289216114.014409448-29.378935877723.289577636
63.748183702851.501664970183.568160171491.447179939931.415291176363.92252270876-0.04705291225210.345853834339-0.0678516768541-0.2248843678090.0831756577765-0.102498303472-0.1134415605210.354553392818-0.03949861826030.2394912427350.001620875058170.03878962188130.2769093226610.02415484951960.172391294813103.803902068-45.3442341951-25.0014877915
70.3784846103010.06912333617580.3833652799510.471802092364-0.1332069947981.502757715050.0155583271850.04912689613850.0307873322114-0.0255544023413-0.0282710836007-0.01332951979950.01150133684430.1221660692760.01462847528690.1814159739940.00317150647775-0.004382971566190.2339775284710.01084197806770.188625816126110.50953204-41.634139592.21554549394
80.4097153421760.291847510480.1834517263971.354593562050.5160990775250.7494346471520.0105148702366-0.002983448289530.0431690551147-0.02854651015870.0082339653229-0.095156908486-0.007331240871090.127552804313-0.02052561393220.155394003262-0.0107237641788-0.001526155757280.2342804424440.01491930374340.175496700367111.7853882-34.11977119249.12780193675
91.363700742280.3225730690040.2286910232770.9515968438550.1173485011420.6501955110790.0434576539775-0.171393019976-0.003016466489770.138876442808-0.0727708033985-0.04019192524450.03274048610880.1168556095280.02069088377410.1755453249140.00107344880675-0.01352888612160.2238465999840.008406270108350.164347275646114.481257199-40.334925878215.5345846667
100.4983904359570.06657952643250.3082225076750.3768149873980.118229396140.8504437705010.04521456433120.0715111728217-0.0363192851609-0.0854835953354-0.0287922361113-0.0174947176530.1080033319210.131657383425-0.01312605406930.2121105952840.0240270020720.002119455854080.200095196265-0.002141010846990.17304271242898.5618710908-54.365732225-11.71596325
110.6453913281060.1374083221920.3071463116680.404416162140.05663068279980.3675170992550.06662625705230.069708473706-0.164171106021-0.0939248042225-0.02745361999640.03748424452730.09963017618580.0662229380704-0.05475794594760.2870581951180.0396745053989-0.01716720860230.21778228925-0.02613999003380.22026419040686.4308647899-64.0934582438-24.1248636543
120.891703316031-1.24878105079-1.329971157325.317325009893.465389201982.996159490240.2082143914430.1236012556890.110458975247-0.518381521385-0.209926102937-0.00310123780354-0.32865553188-0.1673800455990.02166164926780.2995388894080.0368385726522-0.05046613104720.1844936517430.03204620930460.20720883033164.9201633471-16.7334671849-18.6465717326
130.678049255647-0.403291962377-0.0887803667092.17221169255-0.1643594382890.455484186890.03074011691640.0368487992548-0.0166109951373-0.150823558547-0.03618146874820.120072793102-0.0261711874982-0.009396921273920.002695799420440.2205130704710.0101537065474-0.0295856543230.189461587575-0.01380482034430.18542430671972.1969166172-44.7778278133-20.7860625423
140.669955541168-0.428022644485-0.3484341500010.7305963442880.267383088410.5759370452260.03313698813720.0567436604979-0.0409606803132-0.0800664888579-0.04637438174140.1332608278060.0434822795277-0.03394279183430.01888003001980.2281635162540.000628831890038-0.03633032133920.180023267153-0.01185988943580.20334486936174.5913433927-50.9750230429-19.9515528225
150.275906609882-0.11635937673-0.1173102576991.256506321840.4450567361240.5569846771040.02021303370370.05321546061770.00752409328932-0.130546924959-0.05460971346540.164628704313-0.0430946179968-0.06392412818290.0370838231010.2101127571180.00575718036766-0.02374448713160.181364886717-0.004241836345860.23842589478962.5716614168-27.6820761002-8.71183513946
16-0.0770302956253-0.69014502771-0.4068005628222.727229757091.939327142271.672271986680.03690735944560.02266384533770.0319246139991-0.0805230808977-0.1123586216740.195063962093-0.0719728349528-0.1348018521890.1170761913840.2099418975990.003208417523250.000801238767550.195125529504-0.006321304079890.28683726095854.6041079416-15.67709982914.76526322313
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 39 through 92 )AA39 - 921 - 54
22chain 'A' and (resid 93 through 163 )AA93 - 16355 - 125
33chain 'A' and (resid 164 through 256 )AA164 - 256126 - 218
44chain 'A' and (resid 257 through 363 )AA257 - 363219 - 325
55chain 'A' and (resid 364 through 1100 )AA - D364 - 1100326 - 359
66chain 'B' and (resid 39 through 63 )BF39 - 631 - 25
77chain 'B' and (resid 64 through 134 )BF64 - 13426 - 96
88chain 'B' and (resid 135 through 201 )BF135 - 20197 - 163
99chain 'B' and (resid 202 through 235 )BF202 - 235164 - 197
1010chain 'B' and (resid 236 through 363 )BF236 - 363198 - 325
1111chain 'B' and (resid 364 through 1100 )BF - I364 - 1100326 - 359
1212chain 'C' and (resid 39 through 63 )CL39 - 631 - 25
1313chain 'C' and (resid 64 through 134 )CL64 - 13426 - 96
1414chain 'C' and (resid 135 through 256 )CL135 - 25697 - 218
1515chain 'C' and (resid 257 through 363 )CL257 - 363219 - 325
1616chain 'C' and (resid 364 through 1100 )CL - O364 - 1100326 - 357

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