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- PDB-8efz: Crystal structure of CcNikZ-II, apoprotein -

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Basic information

Entry
Database: PDB / ID: 8efz
TitleCrystal structure of CcNikZ-II, apoprotein
ComponentsExtracellular solute-binding protein family 5
KeywordsTRANSPORT PROTEIN / NICKEL IMPORT / METAL TRANSPORT / ABC-TYPE TRANSPORT / SUBSTRATE BINDING PROTEIN / SBP PROTEIN
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Extracellular solute-binding protein family 5
Similarity search - Component
Biological speciesClostridium carboxidivorans P7 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsStogios, P.J. / Evdokimova, E. / Diep, P. / Yakunin, A. / Mahadevan, K. / Savchenko, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies.
Authors: Diep, P. / Stogios, P.J. / Evdokimova, E. / Savchenko, A. / Mahadevan, R. / Yakunin, A.F.
History
DepositionSep 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular solute-binding protein family 5
B: Extracellular solute-binding protein family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4454
Polymers113,3742
Non-polymers712
Water3,081171
1
A: Extracellular solute-binding protein family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7222
Polymers56,6871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular solute-binding protein family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7222
Polymers56,6871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.606, 110.942, 73.686
Angle α, β, γ (deg.)90.000, 113.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Extracellular solute-binding protein family 5


Mass: 56686.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium carboxidivorans P7 (bacteria)
Gene: CcarbDRAFT_1393 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: C6PRH6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30 mg/mL protein and reservoir solution 0.1 M Hepes pH 7.5, 30% (w/v) polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. obs: 40340 / % possible obs: 93.9 % / Redundancy: 4.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.057 / Net I/σ(I): 20.66
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 1752 / CC1/2: 0.652 / Rpim(I) all: 0.267 / % possible all: 81.6

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
MrBUMPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OET

4oet


Resolution: 2.38→29.71 Å / Cross valid method: FREE R-VALUE / σ(F): 0.65 / Phase error: 29.7277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2057 5.27 %RANDOM
Rwork0.2221 37001 --
obs0.2284 39058 90.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.75 Å2
Refinement stepCycle: LAST / Resolution: 2.38→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7781 0 2 171 7954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00237952
X-RAY DIFFRACTIONf_angle_d0.544610716
X-RAY DIFFRACTIONf_chiral_restr0.04421141
X-RAY DIFFRACTIONf_plane_restr0.00331374
X-RAY DIFFRACTIONf_dihedral_angle_d17.95112976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.3637910.33281775X-RAY DIFFRACTION58.01
2.44-2.510.35941230.32932400X-RAY DIFFRACTION77.72
2.51-2.580.34831310.31032530X-RAY DIFFRACTION82.49
2.58-2.660.35191370.29782658X-RAY DIFFRACTION85.19
2.66-2.760.30051380.28162610X-RAY DIFFRACTION84.99
2.76-2.870.3051390.27442662X-RAY DIFFRACTION86.04
2.87-30.28121430.27912667X-RAY DIFFRACTION86.48
3-3.160.30891480.26182747X-RAY DIFFRACTION88.5
3.16-3.350.24651480.24512793X-RAY DIFFRACTION89.58
3.35-3.610.25431450.23872778X-RAY DIFFRACTION90.28
3.61-3.980.25961500.21352830X-RAY DIFFRACTION91.06
3.98-4.550.22371520.1932867X-RAY DIFFRACTION91.98
4.55-5.720.22891520.17782902X-RAY DIFFRACTION92.95
5.73-29.710.25111520.19032890X-RAY DIFFRACTION91.34
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)
12.638142446840.0243001184646-0.3610051194550.849683157883-0.1160672192990.337562096072-0.1473371580770.163926836048-0.0745973790545-0.05023789822880.1356280252050.01350473941790.02503011637420.1183827778120.02477366852620.302139687317-0.0297394848443-0.06532308327530.530832321199-0.03904480663560.20651678296712.0132344935-8.84664115398-43.5540588417
21.923594194670.3444582793482.379695621124.75715217081.127171236332.986374472280.141924640434-0.154701544264-0.03784265025010.510303188025-0.172789399983-0.06377751143420.003766457595150.2674783671280.0358512413330.280736753586-0.01773285560140.00597366990410.5948834334630.02938239319610.26216317606822.4342131675-4.34955790854-34.6426809679
31.52807301706-1.211519973440.03219915083981.9334030595-1.443856603613.27995995380.02180220345620.3567216811260.119905415414-0.04687229665850.1821466597290.147651569511-0.118856414610.297244078881-0.1908888857950.291763568326-0.0458946293091-0.08013909958430.55672473223-0.02701593847520.20542195947113.67549840860.976735111015-41.5338460738
41.703158050120.4717587021910.4013354616122.10707800236-0.2649645777413.230985182690.04356425466710.1788153367790.271023021276-0.1507250625670.1633626250290.3874452120510.0239569958124-0.155251117174-0.1642156158530.2573035141530.0152674926093-0.09468989461120.4390769046030.0002855294869870.274885191069-7.78906159844-5.94512121283-47.2918528752
50.943871596324-0.206560709833-0.4838487710510.973035520847-0.4048450992062.719719188140.0893116691547-0.487328625936-0.1599539398920.08480236777430.1033200888410.2041110369670.37654619384-0.330267047376-0.1629653749010.357042967928-0.0788042703247-0.01313226602160.5679058243930.06255548035530.293756542624-6.98199293263-19.5762954996-15.4382738065
65.69472124432-0.890294923204-1.848915612974.63065638032.920188003412.173313492730.2194020020910.4552423475140.0527080617663-0.2636886797080.158476829694-0.1732356577910.0113328546624-0.192499741394-0.4439025137630.329748790379-0.0185430731892-0.04973913219940.5589011716990.0908485937610.332605578573-13.8347231784-9.42358558476-15.4818001972
72.152146523460.5393280106920.3899156409270.902454586595-0.3831409794853.685415076170.203855670907-0.400373665324-0.3278635377-0.00327972485862-0.0532095512730.00742973570520.240262295010.0217348701993-0.1187811260610.2831206893060.00579706319855-0.02229101737780.4292348051240.01862515318440.2590068391363.80802810744-15.8940467091-26.9133483091
80.401914209236-0.288221136243-0.04888898461961.445822772450.4129921145561.236264849510.04096721124170.2269562987390.06744637000870.01438908915710.0543477897578-0.06685778511040.04196043859070.127599689821-0.1007568895740.2683730020350.00230816610944-0.02913128182270.631324679628-0.03101318385410.2942740727167.67071115284-44.2923578528-69.9706243916
92.8413749829-2.6897077329-0.008517258315886.18047460772-2.771876037012.903297532990.2681604674660.214560975524-0.0486336640117-0.200904673909-0.07024635393990.1615254895350.04633441865480.341604376035-0.1804568059690.274308674906-0.0603995780361-0.07265568998030.735059637349-0.08297382592880.2581272898648.37279304265-47.20760441-76.0609628374
102.00629463514-0.7133182737090.201699037620.690805140055-0.03921148849311.51049395371-0.17278536485-0.05890959393990.101019523860.1705381316790.0642217198828-0.00929875382143-0.0261146948364-0.06399167820820.1027482163560.284167785650.00322713472312-0.04108373956770.352966615873-0.02231850860080.268726888742-5.40028480546-40.4168855474-52.9973822416
111.12064420923-1.008933242070.1498144088170.935791073316-0.3400275267151.01590549697-0.23722722080.0001633226920180.2960113162840.4388856115570.123191493278-0.0358309054458-0.276126373894-0.300241507620.0907736840230.606609243040.113246037158-0.03111910804910.437294080442-0.025023744760.525740473066-25.3611528266-24.9698507633-64.3948453133
124.302401396951.45635327516-0.2499822264912.801649801450.5465482952433.282707780770.02352137009190.0128313901780.4832457766110.323894384187-0.04351597813430.07618154461790.2325828776670.0894855035805-0.01888199759070.4049191746820.04460552831660.03911920886330.48446957379-0.00650980567490.282987905923-31.5169147973-39.6687587031-57.2746863203
139.351256468224.91331654812-0.8434962680766.43457965931.505510430345.42173068816-0.284234903587-0.32134284003-0.7224028755420.9862109422910.4274060797530.1831521238970.0320187824622-0.441675016682-0.06316666492060.5241856909740.1891472380390.08410060936160.6924587558340.0798654923560.348133263739-23.0459857986-47.27153359-60.1821875176
146.15932260150.03291195555221.500402126010.221827284154-0.6007461458645.58450890420.3415197195831.006038363390.0899756640878-0.388669905279-0.241059278914-0.1992950294220.8277376437540.152683510695-0.1021297190.3800780672050.128124094653-0.02958929606760.626342347224-0.02678404846080.339269410665-12.2324656454-36.237702321-76.0801615325
154.09439045408-0.2290149016370.2899698412011.06509798969-0.6902526595383.25798839781-0.19620913928-0.01600337082270.1636568353180.01692685960520.191874945650.0241329181483-0.310792217361-0.2098564447340.03685978018170.2881611649860.0104350065672-0.04395220349380.216981490744-0.04749145527980.281292370431-4.65491969226-31.5971108038-60.731876297
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 86 )AA11 - 861 - 76
22chain 'A' and (resid 87 through 132 )AA87 - 13277 - 122
33chain 'A' and (resid 133 through 168 )AA133 - 168123 - 158
44chain 'A' and (resid 169 through 233 )AA169 - 233159 - 223
55chain 'A' and (resid 234 through 337 )AA234 - 337224 - 323
66chain 'A' and (resid 338 through 373 )AA338 - 373324 - 359
77chain 'A' and (resid 374 through 497 )AA374 - 497360 - 479
88chain 'B' and (resid 11 through 118 )BB11 - 1181 - 108
99chain 'B' and (resid 119 through 157 )BB119 - 157109 - 147
1010chain 'B' and (resid 158 through 293 )BB158 - 293148 - 283
1111chain 'B' and (resid 294 through 320 )BB294 - 320284 - 310
1212chain 'B' and (resid 321 through 364 )BB321 - 364311 - 351
1313chain 'B' and (resid 365 through 390 )BB365 - 390352 - 377
1414chain 'B' and (resid 391 through 435 )BB391 - 435378 - 422
1515chain 'B' and (resid 436 through 496 )BB436 - 496423 - 483

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