PDB-9ll2: Crystal structure of the Helicobacter pylori copper resistance de...

ID or keywords:

Entry

Database: PDB / ID: 9ll2

Title

Crystal structure of the Helicobacter pylori copper resistance determinant CrdA in the apo form

Components

Copper resistance protein

Keywords

METAL BINDING PROTEIN / CrdA / copper ion

Function / homology

:

Function and homology information

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Ki, D.W. / Oh, H.B. / Cho, H.Y. / Song, W.S. / Yoon, S.I.

Funding support

Korea, Republic Of, 1items

Citation

Journal: 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

Deposition	Jan 17, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ll2.cif.gz	120 KB	Display	PDBx/mmCIF format
PDB format	pdb9ll2.ent.gz	76.5 KB	Display	PDB format
PDBx/mmJSON format	9ll2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ll2_validation.pdf.gz	437.1 KB	Display	wwPDB validaton report
Full document	9ll2_full_validation.pdf.gz	438 KB	Display
Data in XML	9ll2_validation.xml.gz	13.1 KB	Display
Data in CIF	9ll2_validation.cif.gz	17.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ll/9ll2 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/9ll2	HTTPS FTP

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Related structure data

Related structure data	9ll4C 9ll5C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Copper resistance protein

B: Copper resistance protein

hetero molecules

24.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Copper resistance protein

hetero molecules

defined by author&software
Evidence: gel filtration
12.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Copper resistance protein

defined by author&software
12.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	37.597, 39.392, 145.404
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	PRO	PRO	(chain 'A' and (resid 18 through 32 or (resid 33...	A	A	18 - 70	3 - 55
1	2	ALA	ALA	LEU	LEU	(chain 'A' and (resid 18 through 32 or (resid 33...	A	A	77 - 125	62 - 110
2	3	LYS	LYS	PRO	PRO	(chain 'B' and (resid 18 through 70 or resid 77...	B	B	18 - 70	3 - 55
2	4	ALA	ALA	LEU	LEU	(chain 'B' and (resid 18 through 70 or resid 77...	B	B	77 - 125	62 - 110

#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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.91 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: ammonium sulfate, bicine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 29, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.64→30 Å / Num. obs: 26939 / % possible obs: 98.6 % / Redundancy: 4.7 % / B_iso Wilson estimate: 17.98 Å² / CC_1/2: 0.994 / Net I/σ(I): 38.4
Reflection shell	Resolution: 1.64→1.67 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1266 / CC_1/2: 0.876 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.64→29.71 Å / SU ML: 0.1365 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.05
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2153	1409	5.24 %
R_work	0.1895	25475	-
obs	0.1909	26884	98.45 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24.25 Å²

Refinement step

Cycle: LAST / Resolution: 1.64→29.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1653	0	15	145	1813

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	1691
X-RAY DIFFRACTION	f_angle_d	0.9312	2286
X-RAY DIFFRACTION	f_chiral_restr	0.0576	258
X-RAY DIFFRACTION	f_plane_restr	0.0058	293
X-RAY DIFFRACTION	f_dihedral_angle_d	10.9463	1048

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.64-1.7	0.2473	132	0.2136	2379	X-RAY DIFFRACTION	94.08
1.7-1.77	0.2409	138	0.2122	2452	X-RAY DIFFRACTION	97.11
1.77-1.85	0.2204	142	0.2053	2471	X-RAY DIFFRACTION	97.35
1.85-1.95	0.227	123	0.1897	2538	X-RAY DIFFRACTION	98.45
1.95-2.07	0.2175	160	0.1783	2526	X-RAY DIFFRACTION	99.15
2.07-2.23	0.2202	134	0.1849	2552	X-RAY DIFFRACTION	99.74
2.23-2.45	0.2466	124	0.1913	2597	X-RAY DIFFRACTION	99.78
2.45-2.81	0.2458	129	0.2055	2610	X-RAY DIFFRACTION	99.89
2.81-3.53	0.2091	135	0.1884	2647	X-RAY DIFFRACTION	99.89
3.53-29.71	0.1927	192	0.1788	2703	X-RAY DIFFRACTION	98.87

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.71811208966	-4.47865881805	5.48289525333	4.24551965785	-5.18391916335	6.57920995143	0.117229998041	0.112387822323	-0.0553760349342	0.198639781567	-0.144077740377	-0.179116384594	-0.0358609207491	0.193780303672	0.133071780943	0.152322885112	-0.00490994925281	0.0105867148846	0.185823396748	-0.0139711408994	0.215907914319	-3.13738068609	2.69970868508	29.4618069979
2	0.398947519301	0.413230952663	0.595850329397	2.95183647077	-0.411855755928	2.00463714933	0.0749054762737	0.0866250468114	0.228040271411	-0.143620751234	-0.0353383344009	-0.249150309254	0.0334064147769	0.0919330010221	-0.0251505916157	0.103978998936	-0.00809440807062	0.0371490228455	0.109266820094	-0.0163784870933	0.0904001169691	-7.51999850105	-1.92926314978	24.9071473447
3	8.26522359378	-5.16588644175	-6.49822052304	6.00132433218	5.62383372159	7.84472666044	-0.154190511548	-0.217318603167	0.157444025974	0.347009601352	-0.0142797568171	0.23201869891	0.0717910206262	-0.226875840005	0.184481765952	0.165558413767	0.00591012817395	-0.000356820410949	0.139813519271	-0.00276579962881	0.149317934831	-18.873795342	-3.51378596822	37.9160786231
4	2.92889174542	-2.40861497222	-1.3754571504	3.46341788159	1.94358451832	2.85065129845	0.0564993274192	0.0749797424636	0.0295255202788	0.0977349865038	-0.0850046984135	0.0893004346444	0.0935036003424	-0.139075493676	0.0371976670761	0.0914716236757	-0.019644828118	0.0217684183241	0.101893003352	0.0145126889506	0.0746292604626	-12.6017741251	-4.26795178318	28.917610127
5	7.17887827555	-7.65634056911	-0.735727561312	9.42360925609	0.645545093064	1.05314403837	-0.0886191350001	0.0218633738478	0.106601338964	0.306247448828	0.0207717409021	-0.231135068655	0.0823034641878	0.083281553447	-0.044654202893	0.100866924044	-0.0217301236099	0.0133979827835	0.142035068121	0.00801358583993	0.124923889153	-4.8788128449	-5.87326607959	34.7312989646
6	6.27501224581	-5.81277036806	3.06864675686	8.78601312791	-5.15348474494	6.44225983346	-0.219944081498	-0.0679643980488	0.254227095229	0.322386372569	0.0468455026334	-0.288881654813	-0.0262464642874	0.23219806981	0.242929591276	0.167568245487	-0.0237249222443	-0.021322415038	0.127435598182	0.0562259121905	0.199893795238	-7.8406671243	6.31556606501	6.40348368442
7	3.51083585555	-1.72463676543	-0.714218039326	7.42021195222	0.458689703956	2.31511250958	0.182411840802	-0.00970977643194	-0.247553380251	-0.0893915893933	-0.143115148802	-0.00350266474461	0.321847656899	0.226949400429	-0.0192660165527	0.181247061733	0.0190733447712	-0.0218781298856	0.124339638707	0.0328424919547	0.0918328571666	-9.6282673666	-1.97479478286	11.4296231502
8	4.58224764863	-2.22842173166	-0.183805596652	7.39903632132	1.01094836073	3.02637532653	0.140225596765	0.100104282948	-0.183433738723	-0.289783361339	-0.203430829987	0.211208993648	-0.0544824325755	-0.154813192536	0.0274423811899	0.153790752127	-0.0129843808591	0.00451613601106	0.134605777759	0.0678441847348	0.0810308814529	-18.2572808127	3.4934321355	6.38452418718
9	2.57487009407	-2.13728392658	0.199407749744	3.53414864097	2.94608737212	5.51700352166	0.102348004082	0.826136989818	-1.0795938406	-1.26622060498	0.451873792136	-0.150922287536	0.0907193881483	0.31906674398	-0.312183232853	0.607636966023	-0.110608776705	0.157252273459	0.472623507501	-0.147077548146	0.554864185258	-11.5411224896	-16.1478619159	-6.02838107398
10	2.79853351027	-2.05372969974	-2.52853945209	5.90865743087	5.62764931917	6.35988062239	-0.0457135244949	0.0147139821267	-0.2280146139	0.368231811221	-0.0349759575648	0.0988383513382	0.494693992096	-0.355763752852	0.146024181793	0.243953468454	-0.012532097468	-0.00074225433307	0.16478698894	0.054407104185	0.165756672997	-19.2959287567	-1.42807788834	10.8684272234
11	2.54510996165	-1.81321985148	-0.270588791435	2.96369214014	0.522393950104	0.97084270211	-0.140440602557	0.00720503006938	-0.279315677284	0.328159076971	0.0500415482593	-0.159218011299	0.527590174124	-0.117917080885	0.095305449769	0.311134852006	0.0256475826191	0.0222292484252	0.132514888341	0.065424154499	0.205861411963	-12.8623999752	-6.89607192391	9.61308155867
12	9.02329156438	-5.37212138628	-1.74518021042	8.16870864983	2.36180928428	1.04087435497	0.244973807202	0.793786290665	0.204172569008	-0.11292186333	-0.366403479035	-0.391553781473	0.043249651634	-0.134330033779	0.0753242150698	0.178060178765	0.0201687305996	0.0148522051719	0.14624669303	0.0384175776917	0.116295426922	-14.9324794547	-1.0528895265	0.991961640257
13	7.47358645364	-6.65795722243	-0.231118729976	8.06860104401	-0.377728432948	2.43211287975	-0.0785029458758	0.211429587675	0.276587722833	0.193482324021	-0.0405313537078	-0.285041154331	0.13228962327	0.0614321226194	0.099801001803	0.11196266489	-0.0134090203069	-0.0204781949339	0.0870692688715	0.00441306267259	0.14802205178	-16.7489353213	5.10201883594	2.13481827233

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 125 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 18 through 36 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 37 through 53 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 54 through 69 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 70 through 78 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 79 through 89 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 90 through 101 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 102 through 110 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 111 through 125 )

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