PDB-3hf7: The Crystal Structure of a CBS-domain Pair with Bound AMP from Kl...

ID or keywords:

Entry

Database: PDB / ID: 3hf7

Title

The Crystal Structure of a CBS-domain Pair with Bound AMP from Klebsiella pneumoniae to 2.75A

Components

uncharacterized CBS-domain protein

Keywords

structural genomics / unknown function / CSB-domain pair / AMP / klebsiella / pneumoniae / PSI / MCSG / Midwest Center for Structural Genomics / Protein Structure Initiative / Cell membrane / Membrane / Transmembrane

Function / homology

Function and homology information

flavin adenine dinucleotide binding / membrane => GO:0016020
Similarity search - Function

Biological species

Klebsiella pneumoniae subsp. pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.75 Å

Authors

Stein, A.J. / Nocek, B. / Wu, R. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of a CBS-domain Pair with Bound AMP from Klebsiella pneumoniae to 2.75A
Authors: Stein, A.J. / Nocek, B. / Wu, R. / Bearden, J. / Joachimiak, A.

History

Deposition	May 11, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hf7.cif.gz	40.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3hf7.ent.gz	28.6 KB	Display	PDB format
PDBx/mmJSON format	3hf7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3hf7_validation.pdf.gz	782.7 KB	Display	wwPDB validaton report
Full document	3hf7_full_validation.pdf.gz	785.5 KB	Display
Data in XML	3hf7_validation.xml.gz	7.5 KB	Display
Data in CIF	3hf7_validation.cif.gz	9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hf/3hf7 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/3hf7	HTTPS FTP

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Related structure data

Similar structure data	2dis-d 2dwx-3 4gpr-d 5ngz-d 4fr9-d 2esq-d 1jbb-1 2c4p-2 4evc-d 1lxn-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC63102.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (2) #140 - Aug 2011 Rhomboid Protease GlpG similarity (3) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: uncharacterized CBS-domain protein

hetero molecules

15.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: uncharacterized CBS-domain protein

hetero molecules

A: uncharacterized CBS-domain protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.395, 101.395, 107.745
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

Details

biological unit is the same as asymmetric unit.

#1: Protein	uncharacterized CBS-domain protein / uncharacterized protein yfjD Mass: 14986.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: MGH 78578 / Gene: yfjD, KPN78578_28800, KPN_02935 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6TCM0
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 65.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 1.8 Magnesium sulfate, 0.1M Bis-tris propane, pH 7.0, vapor diffusion, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2006

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 9474 / % possible obs: 98.1 % / Redundancy: 5.5 % / R_merge(I) obs: 0.092 / Χ²: 1.478 / Net I/σ(I): 7.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.3-2.38	5.7	0.66	945	0.713	1	100
2.38-2.48	5.7	0.47	951	0.723	1	100
2.48-2.59	5.7	0.324	951	0.763	1	100
2.59-2.73	5.7	0.23	958	0.894	1	100
2.73-2.9	5.7	0.162	964	1.006	1	100
2.9-3.12	5.7	0.125	953	1.232	1	100
3.12-3.44	5.6	0.099	972	1.612	1	100
3.44-3.93	5.2	0.086	781	2.128	1	82
3.93-4.95	5.3	0.077	988	2.724	1	99.9
4.95-50	4.9	0.076	1011	3.426	1	99.1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0054	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		phasing
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 2.75→50 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.914 / WR_factor R_free: 0.292 / WR_factor R_work: 0.239 / SU B: 29.126 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.278	270	4.9 %	RANDOM
R_work	0.222	-	-	-
obs	0.225	5517	96.79 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.833 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.49 Å²	-2.25 Å²	0 Å²
2-	-	-4.49 Å²	0 Å²
3-	-	-	6.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	972	0	23	5	1000

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	1011
X-RAY DIFFRACTION	r_angle_refined_deg	1.406	1.998	1382
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.174	5	126
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.805	24.091	44
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.688	15	161
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.852	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	168
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	750
X-RAY DIFFRACTION	r_mcbond_it	0.398	1.5	631
X-RAY DIFFRACTION	r_mcangle_it	0.777	2	1020
X-RAY DIFFRACTION	r_scbond_it	1.388	3	380
X-RAY DIFFRACTION	r_scangle_it	2.444	4.5	362

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.75-2.822	0.363	35	0.26	374	409	100
2.822-2.899	0.383	17	0.282	396	413	100
2.899-2.983	0.182	15	0.277	381	396	100
2.983-3.074	0.392	19	0.317	357	376	100
3.074-3.175	0.354	13	0.27	340	353	100
3.175-3.286	0.355	23	0.281	352	375	100
3.286-3.41	0.36	12	0.274	325	337	100
3.41-3.549	0.406	25	0.254	306	331	100
3.549-3.706	0.461	8	0.23	188	334	58.683
3.706-3.886	0.348	11	0.222	267	312	89.103
3.886-4.096	0.225	9	0.208	274	283	100
4.096-4.343	0.317	12	0.17	271	283	100
4.343-4.642	0.286	14	0.168	250	265	99.623
4.642-5.012	0.23	10	0.185	227	237	100
5.012-5.487	0.243	13	0.198	218	231	100
5.487-6.13	0.225	9	0.248	204	213	100
6.13-7.069	0.131	8	0.218	173	181	100
7.069-8.634	0.183	5	0.201	159	164	100
8.634-12.113	0.199	8	0.156	114	126	96.825
12.113-68.041	0.102	4	0.262	71	81	92.593

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	0.3702	0.518	-0.3182	4.6381	-0.3611	0.5233	0.0673	0.1408	0.3683	-0.0543	0.0041	0.0286	-0.2393	-0.1639	-0.0714	0.4895	0.1788	-0.0645	0.3333	0.0896	0.7014	50.2909	0.8511	21.9357
2	6.1697	0.0763	3.1539	3.9206	-0.6953	2.9493	0.0173	0.6588	-0.1297	-0.8025	-0.0741	-0.014	0.061	0.047	0.0568	0.357	0.0134	0.0414	0.3693	-0.0027	0.4368	48.3908	13.0777	20.4342
3	5.87	-0.7899	2.2256	6.1235	-0.5734	0.8672	0.2459	0.3358	-0.0092	-0.9471	-0.23	-0.51	0.0931	0.1128	-0.0159	0.4675	-0.0044	0.0723	0.3473	0.018	0.498	41.6533	20.1498	20.7951
4	10.8629	-5.5146	5.0721	2.9374	-1.9931	4.8393	-0.1855	0.1164	0.2119	0.0421	0.0355	-0.1084	-0.3633	0.4343	0.15	0.3889	-0.0074	-0.0142	0.3435	-0.0138	0.4298	34.9459	31.2161	24.6935
5	11.0243	7.6339	5.6443	8.0991	7.764	11.0782	-0.3009	0.9444	0.2647	-0.7503	0.3248	-0.184	-0.1483	0.2332	-0.0239	0.4715	0.0769	0.0832	0.3605	0.0353	0.444	33.5074	28.533	18.7892
6	6.0771	-1.6634	-2.0981	1.7489	-1.8417	5.8912	-0.0116	0.1882	-0.1767	-0.2919	0.123	0.1097	0.0892	0.0042	-0.1115	0.5469	-0.1512	-0.0236	0.464	-0.0509	0.4743	32.9572	18.2134	17.1436
7	8.0358	-0.798	-3.0293	10.0374	-4.3062	3.2737	-0.0098	0.0458	0.015	0.0264	-0.0145	-0.0559	-0.0173	-0.0085	0.0243	0.3659	-0.0539	0.0052	0.336	0.0133	0.4202	39.1142	21.8709	27.1729
8	1.2183	-2.1613	1.6925	8.9068	-5.7205	5.6721	0.0752	0.0094	0.4089	0.3178	-0.1323	-0.7782	-0.107	0.8703	0.0571	0.3547	-0.0659	-0.0295	0.5983	-0.0949	0.6806	45.6483	22.7113	29.7041
9	7.2935	0.0985	1.7494	4.0766	0.6495	9.2122	0.0198	-0.1985	0.0715	0.0036	-0.1993	0.3517	0.1939	-0.5193	0.1796	0.3131	-0.0022	0.0176	0.2798	0.0034	0.3787	32.8314	16.6821	26.8757
10	0.9974	-3.174	-0.2819	11.0993	3.0007	10.8314	-0.087	-0.2143	-0.2507	0.3631	0.1535	0.6161	0.1555	-0.3775	-0.0665	0.371	-0.0219	-0.0397	0.4584	0.0162	0.5271	23.5294	17.8357	22.2847
11	1.1842	0.5611	-0.5354	0.5941	1.2551	7.6509	0.0236	-0.3617	0.1141	-0.0149	-0.3276	0.1771	0.0268	-0.9213	0.304	0.4142	0.0188	0.0111	0.4856	0.0452	0.71	19.6877	25.5847	23.9745
12	11.6397	-5.0793	-9.1344	6.5572	3.7909	7.2695	0.2109	-0.4796	0.4258	0.7003	0.043	0.3824	-0.3079	0.2197	-0.2539	0.3945	0.0604	-0.0352	0.4311	-0.0999	0.4745	27.7068	26.5207	30.1695
13	7.2471	-6.9719	-2.7968	15.7573	3.8164	1.6828	-0.2162	-0.3523	-0.173	0.7188	0.2189	0.3199	0.1518	0.1022	-0.0027	0.3394	-0.012	-0.006	0.3477	0.013	0.3671	30.2257	18.4012	32.4913
14	3.144	-4.7847	-1.3871	7.3245	1.7174	5.95	-0.096	-0.128	0.3135	0.112	0.1328	-0.5619	0.3352	0.3671	-0.0368	0.2942	-0.0232	0.0189	0.3151	0.0572	0.5795	44.012	7.8183	31.4271
15	0.6042	1.7487	-1.166	6.9119	-4.2378	10.8413	-0.1975	-0.0758	-0.1908	0.0902	-0.0872	-0.1388	1.0236	0.2743	0.2848	0.5102	0.0153	-0.008	0.3719	0.0072	0.8485	46.2114	-2.2619	27.6433
16	1.9138	-1.019	4.1339	1.7205	-3.3995	10.1539	0.942	-0.4965	0.1897	-0.5657	-0.3732	0.9634	1.9475	-0.3312	-0.5688	0.7225	-0.2279	-0.1858	1.1982	-0.1295	1.5159	37.8181	-1.9722	29.6851
17	9.2051	4.5519	1.7858	7.0942	-2.0397	3.705	-0.0868	0.493	0.5252	-0.1209	0.1014	-0.1192	-0.3187	0.329	-0.0146	0.4271	-0.2648	0.1502	0.5053	0.1282	0.6586	38.3977	6.579	27.6641
18	5.0722	-3.0268	8.0513	3.1577	-3.9278	14.8037	0.0614	0.2437	-0.036	0.1249	-0.0875	-0.6416	0.3135	0.9182	0.0261	0.3497	-0.021	0.0147	0.4391	0.0778	0.5283	52.2588	12.3687	32.4596
19	5.2853	4.6964	1.303	4.2917	1.6244	2.3605	-0.1224	0.3903	-0.13	-0.0227	0.3112	-0.1438	0.1145	0.1179	-0.1888	0.3407	-0.0327	0.0127	0.3117	-0.0607	0.6716	42.3387	5.2619	21.9861
20	15.8732	1.6613	-9.2692	1.4668	1.7332	16.7584	-0.0885	0.6431	-0.1668	-0.3648	0.2063	-0.377	0.0313	0.2812	-0.1178	0.5829	0.0652	0.0533	0.4398	0.0013	0.6191	41.5581	-4.3654	16.2943

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	201 - 207
2	X-RAY DIFFRACTION	2	A	208 - 212
3	X-RAY DIFFRACTION	3	A	213 - 218
4	X-RAY DIFFRACTION	4	A	219 - 224
5	X-RAY DIFFRACTION	5	A	225 - 229
6	X-RAY DIFFRACTION	6	A	230 - 237
7	X-RAY DIFFRACTION	7	A	238 - 242
8	X-RAY DIFFRACTION	8	A	243 - 248
9	X-RAY DIFFRACTION	9	A	249 - 254
10	X-RAY DIFFRACTION	10	A	255 - 260
11	X-RAY DIFFRACTION	11	A	261 - 267
12	X-RAY DIFFRACTION	12	A	268 - 272
13	X-RAY DIFFRACTION	13	A	273 - 278
14	X-RAY DIFFRACTION	14	A	279 - 284
15	X-RAY DIFFRACTION	15	A	285 - 291
16	X-RAY DIFFRACTION	16	A	292 - 297
17	X-RAY DIFFRACTION	17	A	298 - 305
18	X-RAY DIFFRACTION	18	A	306 - 312
19	X-RAY DIFFRACTION	19	A	313 - 321
20	X-RAY DIFFRACTION	20	A	322 - 327

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