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- PDB-9ll4: Crystal structure of the Helicobacter pylori copper resistance de... -

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Basic information

Entry
Database: PDB / ID: 9ll4
TitleCrystal structure of the Helicobacter pylori copper resistance determinant CrdA in complex with silver ions in space group P21
ComponentsCopper resistance protein
KeywordsMETAL BINDING PROTEIN / CrdA / copper ion
Function / homologySILVER ION / :
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKi, D.W. / Oh, H.B. / Cho, H.Y. / Song, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
CitationJournal: Febs J. / Year: 2025
Title: Structural basis of Cu(I) ion recognition by the Helicobacter pylori copper resistance determinant CrdA.
Authors: Ki, D.U. / Oh, H.B. / Cho, H.Y. / Song, W.S. / Yoon, S.I.
History
DepositionJan 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper resistance protein
B: Copper resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0767
Polymers24,5492
Non-polymers5285
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-34 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.229, 39.026, 65.099
Angle α, β, γ (deg.)90.000, 102.108, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain 'A' and (resid 20 through 27 or (resid 28...AA20 - 275 - 12
12LEULEUGLUGLU(chain 'A' and (resid 20 through 27 or (resid 28...AA30 - 7115 - 56
13PROPROGLUGLU(chain 'A' and (resid 20 through 27 or (resid 28...AA73 - 8658 - 71
14GLYGLYLEULEU(chain 'A' and (resid 20 through 27 or (resid 28...AA89 - 12574 - 110
25PROPROALAALA(chain 'B' and (resid 20 through 25 or (resid 26...BB20 - 275 - 12
26LEULEUGLUGLU(chain 'B' and (resid 20 through 25 or (resid 26...BB30 - 7115 - 56
27PROPROGLUGLU(chain 'B' and (resid 20 through 25 or (resid 26...BB73 - 8658 - 71
28GLYGLYLEULEU(chain 'B' and (resid 20 through 25 or (resid 26...BB89 - 12574 - 110

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Components

#1: Protein Copper resistance protein


Mass: 12274.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: B0X44_01495, B0X54_06630 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A6UQS9
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: ammonium sulfate, citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 17430 / % possible obs: 96.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 24.58 Å2 / CC1/2: 0.99 / Net I/σ(I): 29.8
Reflection shellResolution: 1.97→2 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 794 / CC1/2: 0.874 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→29.84 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2493 817 4.69 %
Rwork0.2005 16596 -
obs0.2028 17413 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.95 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 5 46 1637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351612
X-RAY DIFFRACTIONf_angle_d0.73482185
X-RAY DIFFRACTIONf_chiral_restr0.0496254
X-RAY DIFFRACTIONf_plane_restr0.0046279
X-RAY DIFFRACTIONf_dihedral_angle_d18.2735993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.090.25171450.21592628X-RAY DIFFRACTION93.75
2.09-2.260.30641500.22332745X-RAY DIFFRACTION97.05
2.26-2.480.24211220.22072794X-RAY DIFFRACTION97.26
2.48-2.840.27881380.2312787X-RAY DIFFRACTION97.6
2.84-3.580.24561320.19832814X-RAY DIFFRACTION97.87
3.58-29.840.22411300.17632828X-RAY DIFFRACTION95.45
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)
16.36384938231-1.55479322437-1.861442219645.160845971985.543251976785.981695217540.1132057039560.06178402837790.0229634842393-0.256377209148-0.2575010591670.175183820542-0.160371820006-0.3053487710560.1499113145850.24203303417-0.003025637257280.04955535806560.1691700208720.01101629052270.169632096823.9695432802910.0357393768-27.5139273362
25.06364768552.45125478043.092850067477.239115841343.169935841976.835555840410.221873310755-0.3281739497020.1705174425590.300207583340.10975898503-0.2066219780470.0456621370425-0.0794780405285-0.2408279260190.153458040239-0.006139664126430.06614976639290.227072606201-0.06207719608540.1900193739060.70660186778111.5145837623-16.4086133493
31.504910204080.162213119104-1.01000950312.172753329052.380651417534.06813343308-0.2709328172550.78343809668-0.192912037091-0.1610531603460.06087406374770.130091692257-0.129222133241-0.004805806128180.1344590726010.203257976527-0.08637239450360.05403828002810.234676232702-0.01756804543790.2011471510381.684115744541.67725253893-24.8388724254
49.572767457139.142632842368.616111702688.743509980918.118881044299.603187330710.4433114978030.898564596116-0.5977926151290.3600475773240.344092085866-0.5061776354270.05038295047560.843951935993-0.8044320792890.2217310331930.0448911938655-0.001337586297650.353767746320.0200342250270.31608177056921.10947310646.00399674341-7.39350706864
54.847176149161.236163440795.433256880721.390855012441.378489706066.282279329990.699078936256-0.771596845236-0.3306179866030.145391799463-0.265745050118-0.2973328833490.891621303454-0.682117420591-0.2806629119480.371683668615-0.107947176380.08488972600690.2854465815280.08857083878140.3559658290288.898779467521.16786511635-11.2650078737
66.447543663714.938146034875.889294988985.189910836225.430215741438.775584740590.0655294039576-0.3155369734660.1070485117680.123161260398-0.2887427470830.2087661432530.179521805328-0.7671576971450.2519008391510.17188752481-0.03227759683170.05301121601910.209738249589-0.008663664992430.162943712076-0.4577795495985.7346104861-15.8738134935
78.183881495386.986672899597.121788156967.210286745166.60695777226.409726795680.1958801470420.231797584934-0.785450224054-0.003598173306050.138498755435-0.3770008719760.4183529060360.211667790981-0.365355043180.19925463878-0.02603256306290.02603055171870.164548046604-0.01272576058220.2506818719286.02538055583-0.168914757605-24.1909138859
84.982710444184.753577169624.173116359334.746886991684.061700101793.58198443942-0.05243110221330.00717656796833-0.3626873350890.06859640346720.184905819748-0.658450308629-0.09302851463430.151763465381-0.179274878390.2418185386510.005076265235740.008753546282050.1378213981060.02697613616880.2207479225299.931160842855.87200820686-23.019878587
96.929247811670.5381126836382.608583833374.6272371608-1.632082576326.49815667380.239963910831-0.265621057419-0.451599775560.0823241718359-0.06896912788150.07431413331990.356047562893-0.130815617251-0.1802704368210.195300999928-0.01708905332940.001506480295880.153565218629-0.01278862171430.17524627787829.861190364320.848696923-3.11138247804
103.097347590061.836927811853.397417717411.821196895580.9407105018315.33051330952-0.0377202415387-0.136338334893-0.170825509057-0.2119186012510.140863701054-0.210348241545-0.006621955673970.191137854976-0.1731803737070.2164174575190.03758408093270.03764764525440.25877772931-0.03629635232270.30634265856836.366772354822.5581390558-9.76497056318
116.462341823027.249664689815.721051054898.270323019277.190919537027.49654935892-0.4987512834350.454880111064-0.0446719091324-0.5134303254630.549604515757-0.110027921037-0.4144624324810.101826126665-0.005614800131340.2620075250340.001155573859310.01950764612750.211373319990.02170882183650.25517670308226.57197713222.1439651257-16.2066848647
123.933239467523.484023870293.740266899355.168491213051.763003327554.73449182065-0.1968391312490.1033193259820.603190104493-0.269196526028-0.009923328569710.63667599046-0.334731456311-0.266318096790.2074761464890.1851298009180.02472889264370.01309231716580.210543712156-0.005528435820260.22758091308825.027548080626.3290800195-10.4473012256
133.927203654693.396835955381.494224389373.000508190851.059655801122.09187217873-0.1054177130830.147061611371-0.260024232180.07369557525340.309614632743-0.2792526283240.0815038929090.354685171476-0.1869461533220.1544968926790.00818312395862-0.01282755728510.222342761204-0.0362176131860.25103719793834.151358528418.0468842569-11.3082844483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 77 )
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 101 )
7X-RAY DIFFRACTION7chain 'A' and (resid 102 through 115 )
8X-RAY DIFFRACTION8chain 'A' and (resid 116 through 125 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 53 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 69 )
11X-RAY DIFFRACTION11chain 'B' and (resid 70 through 89 )
12X-RAY DIFFRACTION12chain 'B' and (resid 90 through 101 )
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 125 )

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