PDB-8dt1: Crystal Structure of a Putative D-beta-hydroxybutyrate dehydrogen...

ID or keywords:

Entry

Database: PDB / ID: 8dt1

Title

Crystal Structure of a Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD

Components

3-hydroxybutyrate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / Putative D-beta-hydroxybutyrate dehydrogenase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

3-hydroxybutyrate dehydrogenase activity / nucleotide binding
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of a Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD
Authors: Abendroth, J. / Mayclin, S.J. / Phan, J.N. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jul 25, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 17, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8dt1.cif.gz	486.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8dt1.ent.gz	330.4 KB	Display	PDB format
PDBx/mmJSON format	8dt1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8dt1_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	8dt1_full_validation.pdf.gz	2.5 MB	Display
Data in XML	8dt1_validation.xml.gz	48.2 KB	Display
Data in CIF	8dt1_validation.cif.gz	68.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dt/8dt1 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/8dt1	HTTPS FTP

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Related structure data

Related structure data	4trrS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (3) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

Deposited unit

A: 3-hydroxybutyrate dehydrogenase

B: 3-hydroxybutyrate dehydrogenase

C: 3-hydroxybutyrate dehydrogenase

D: 3-hydroxybutyrate dehydrogenase

hetero molecules

119 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	59.910, 65.600, 68.320
Angle α, β, γ (deg.)	97.149, 98.382, 107.470
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	3-hydroxybutyrate dehydrogenase Mass: 28444.488 Da / Num. of mol.: 4 / Fragment: BuceA.00010.z.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: A8E72_04365, A8F33_24625 / Plasmid: BuceA.00010.z.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V2Y0M0

#1: Protein

3-hydroxybutyrate dehydrogenase

Mass: 28444.488 Da / Num. of mol.: 4 / Fragment: BuceA.00010.z.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia cenocepacia (bacteria) / Gene: A8E72_04365, A8F33_24625 / Plasmid: BuceA.00010.z.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V2Y0M0

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Non-polymers , 5 types, 755 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 738 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Optimized condition around RigakuReagents JCSG+ screen, condition C6:100mM sodium phosphate dibasic/citric acid pH 4.5: 43% (V/V) PEG 300: BuceA.00010.z.B1.PS01812 at 40mg/ml + 5mM NAD/MgCl2: ...Details: Optimized condition around RigakuReagents JCSG+ screen, condition C6:100mM sodium phosphate dibasic/citric acid pH 4.5: 43% (V/V) PEG 300: BuceA.00010.z.B1.PS01812 at 40mg/ml + 5mM NAD/MgCl2: tray: 325332 H9: cryo: reservoir with 5mM NAD and MgCl2: puck jqn3-2.

Crystal

Density Matthews: 2.2 Å³/Da / Density % sol: 44 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Optimized condition around RigakuReagents JCSG+ screen, condition C6:100mM sodium phosphate dibasic/citric acid pH 4.5: 43% (V/V) PEG 300: BuceA.00010.z.B1.PS01812 at 40mg/ml + 5mM NAD/MgCl2: ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 18, 2022 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 88982 / % possible obs: 99.3 % / Redundancy: 3.195 % / B_iso Wilson estimate: 27.47 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.042 / R_rim(I) all: 0.05 / Χ²: 0.826 / Net I/σ(I): 15.91

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.8-1.85	1.873	0.297	2.46	6505	0.891	0.396	97.5
1.85-1.9	2.038	0.244	3.26	6354	0.916	0.318	98.4
1.9-1.95	2.249	0.208	4.11	6209	0.943	0.265	98.9
1.95-2.01	2.436	0.164	5.41	6096	0.963	0.206	99.5
2.01-2.08	2.65	0.138	6.82	5838	0.971	0.171	99.6
2.08-2.15	2.889	0.106	9.08	5743	0.985	0.129	99.6
2.15-2.23	3.105	0.088	11.42	5463	0.99	0.105	99.7
2.23-2.32	3.373	0.079	12.84	5319	0.993	0.093	99.7
2.32-2.43	3.82	0.07	15.3	5061	0.995	0.081	99.8
2.43-2.55	4.033	0.063	17.44	4872	0.996	0.073	99.9
2.55-2.68	4.032	0.055	19.41	4617	0.997	0.063	100
2.68-2.85	4.045	0.046	22.01	4414	0.998	0.053	99.9
2.85-3.04	4.024	0.04	25.07	4074	0.998	0.046	99.8
3.04-3.29	4.017	0.035	28.03	3833	0.998	0.04	99.9
3.29-3.6	4.006	0.029	33.32	3512	0.999	0.033	99.7
3.6-4.02	3.973	0.026	37.02	3192	0.999	0.03	99.9
4.02-4.65	3.903	0.024	39.37	2807	0.999	0.028	99.5
4.65-5.69	3.812	0.026	38.4	2317	0.998	0.031	98.6
5.69-8.05	3.636	0.03	37.64	1791	0.998	0.036	98
8.05-50	3.209	0.032	38.43	965	0.997	0.038	95.6

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.20.1	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: apo structure, PDB entry 4trr

4trr

Resolution: 1.8→22.17 Å / SU ML: 0.1398 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.4806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1779	2013	2.26 %	0
R_work	0.1461	86931	-	-
obs	0.1468	88944	99.38 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 26.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→22.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7311	0	301	738	8350

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	8000
X-RAY DIFFRACTION	f_angle_d	0.9392	10948
X-RAY DIFFRACTION	f_chiral_restr	0.0616	1306
X-RAY DIFFRACTION	f_plane_restr	0.0075	1525
X-RAY DIFFRACTION	f_dihedral_angle_d	14.3389	2925

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 (%)
1.8-1.85	0.2387	138	0.1934	6129	X-RAY DIFFRACTION	97.56
1.85-1.89	0.2136	148	0.1847	6129	X-RAY DIFFRACTION	98.34
1.89-1.95	0.2218	140	0.1742	6190	X-RAY DIFFRACTION	98.89
1.95-2.01	0.198	126	0.1585	6238	X-RAY DIFFRACTION	99.59
2.01-2.09	0.1511	132	0.1456	6181	X-RAY DIFFRACTION	99.67
2.09-2.17	0.1835	155	0.1369	6222	X-RAY DIFFRACTION	99.69
2.17-2.27	0.1811	143	0.1406	6286	X-RAY DIFFRACTION	99.64
2.27-2.39	0.184	148	0.1453	6208	X-RAY DIFFRACTION	99.75
2.39-2.54	0.1832	177	0.1493	6231	X-RAY DIFFRACTION	99.97
2.54-2.73	0.1824	148	0.1522	6238	X-RAY DIFFRACTION	100
2.73-3.01	0.199	141	0.1525	6235	X-RAY DIFFRACTION	99.94
3.01-3.44	0.1987	146	0.1487	6212	X-RAY DIFFRACTION	99.91
3.44-4.33	0.1465	135	0.1265	6252	X-RAY DIFFRACTION	99.84
4.33-22.17	0.1485	136	0.1393	6180	X-RAY DIFFRACTION	98.49

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	3.70896452203	0.699031181316	-1.52683849679	1.96178225951	-0.18684897557	2.72799661543	0.131334056815	0.401617972507	0.268539503959	-0.247297544045	0.0777321052837	-0.289162415128	-0.33199838492	0.106142178867	-0.209549962595	0.151367492832	-0.0515578957833	0.0567165268486	0.179446295492	0.00224931143371	0.20812395026	9.4910434337	49.5741981287	0.747784396716
2	3.39393614401	-0.621848557195	-2.3568354583	3.40882093691	2.50121570906	6.93535671085	0.389077963076	0.414513804828	0.717117757957	-0.396842509518	-0.0117905938817	-0.0248439379604	-0.754631363673	-0.168036547115	-0.309236643569	0.222713896658	0.02984835489	0.0792414337283	0.184996873549	0.0887480713613	0.336492228891	-2.55493653163	54.1829388103	-0.0989403754874
3	1.02034127159	-0.0580275152251	0.470035065714	1.82718725996	0.162345786764	3.19185831687	0.100470488934	-0.0787746279953	0.10751351386	0.143874398003	0.00376798644083	-0.165317229018	-0.120290991674	0.058332242802	-0.086073293407	0.0857231978979	-0.0157550861638	0.0119472778445	0.109654390896	-0.00163055771451	0.158224417544	-3.01582326355	44.5018514412	14.8640386534
4	1.69145723283	-0.097467031752	0.632951926784	1.96806537648	-0.0157461053878	3.07175566015	0.0937941123831	0.0373760341124	0.0457741599542	-0.0578945435824	-0.0212194161904	0.0430989703254	-0.0286670698814	0.00378522020147	-0.0718347773412	0.0699924354923	0.00780458633385	0.00748066344437	0.0689849339909	-0.00451818906027	0.123438491788	-7.5905517774	36.4775994267	9.69220112236
5	2.37398060587	0.0230192393935	0.4694736779	3.03039248897	0.0455602954933	3.77063224102	0.256939066461	-0.554738130706	-0.182634418496	0.332021880408	-0.0551742361323	-0.585476960259	0.0422674672152	0.378549730544	-0.17765900293	0.127268904483	-0.044036805149	-0.0267024693829	0.225578224467	0.0113732457286	0.224066398562	6.98938772187	33.4532204358	14.5851747822
6	5.77526729153	0.780093725386	-2.54059399485	7.51756902801	-3.93708022303	7.12972161843	0.276684462859	-0.851056575471	0.342374535103	1.01273067435	-0.241918716448	-0.680567633343	-0.396510746944	0.949990332267	-0.0546017549639	0.239538438724	0.000617531968944	-0.0714382837463	0.316795420869	-0.0235593179592	0.28432876384	10.615930168	23.3191393216	16.9597935192
7	1.06149218938	0.395128179279	0.0368411602541	1.87658925171	-0.219014800763	1.88878076047	0.00326701484946	0.000880407623454	0.0085224244648	-0.00844082271288	0.00997263860106	-0.182659756758	-0.0081022532896	0.112071280441	-0.011095874992	0.0797992445253	0.0143504392861	-0.00567374821259	0.091736264811	-0.00650400303629	0.139937047071	-0.372857477534	27.3824314022	4.3698300815
8	1.11755649017	-0.130272852518	0.00187466502953	1.23591186422	-0.0815961434899	1.44196859798	0.0193879195158	-0.264632611894	0.0616078102138	0.443874874085	0.0192558801251	0.147297842493	-0.134600095384	-0.118979632198	-0.0351558399406	0.250002890041	0.00966621702823	0.0590949697808	0.173640344407	-0.0225350322976	0.135585961627	-18.0580619518	39.7918723177	31.9949163643
9	4.20584308782	-0.00675954278728	2.40809222078	1.12264269272	-0.296967120935	3.47980605226	-0.161403278535	0.0324590726027	0.310443360417	0.137859286078	-0.00519230476137	0.314134345431	-0.188111129082	-0.281214094226	0.147885124186	0.14942928444	0.00146372706222	0.0298025751588	0.133373693739	-0.0135848454371	0.220414304556	-26.8370112162	29.0836489685	21.8054932827
10	1.02266672454	0.683533340966	-0.329056598875	0.65340760848	0.239688256986	2.25449819538	0.126059210843	-0.267191209306	-0.221173462113	0.851091627762	-0.278932689001	0.294119185714	0.99933030901	-0.275242134419	0.167412508298	0.571609811231	-0.147615747702	0.173912769275	0.267252421934	0.00853686687967	0.223852717215	-25.302423915	-2.30498431567	32.8126337793
11	1.8361035347	-0.38488202036	-0.320099764199	1.17407461002	0.38697368204	1.00415780745	-0.0951681906258	-0.0989365884125	-0.0490196506325	0.198253043982	-0.00624121967937	0.159865848383	0.209630502437	-0.0977609088984	0.0904385859483	0.155358185563	-0.0262769336329	0.0226858081746	0.114976361464	0.00730500888311	0.115152410108	-16.9556081249	4.59112584164	18.8675562814
12	4.42923747661	0.431858916864	0.557729449032	2.7996198637	0.353162567004	3.11692697637	-0.110996239722	-0.233576153993	-0.364254566787	0.542512999156	-0.047374166755	-0.24089193012	0.184646250189	0.313192006972	0.142633012166	0.289292218073	-0.0143843209652	0.0323865193241	0.162592215399	0.0442950853104	0.162725226388	-13.0062546081	9.06748570388	30.3982576504
13	4.02456629157	-2.35733136404	-0.328499730189	5.91122741073	-0.757997279515	1.88037364245	-0.391734385826	-0.760950970254	-0.528575034296	0.42145509874	-0.201591305058	-1.29284881912	0.541358359886	0.87055838557	0.38730466106	0.400616765282	0.0890341649856	-0.06211720275	0.437504484556	0.154480725775	0.422931030811	1.28794305419	12.7381337132	35.6651022008
14	3.090267318	0.565806145152	0.611208266217	1.87838331326	-0.281072195171	2.09158796224	0.0260855821316	-0.235585918286	0.0835062058735	0.340632929659	-0.050104815277	0.113283825983	0.215753604136	-0.0944282141924	0.0246002385818	0.195282382818	-0.00813993537329	0.0173680675602	0.0937210165181	-0.0227997942412	0.127857882633	-18.0729848039	16.9961634112	29.1094105553
15	2.33669125698	-0.451680849887	-0.441447795284	1.89019208048	-0.456681573039	3.34981095165	-0.0452610668282	0.476215563834	0.0276573598343	-0.56753473964	-0.0283195791757	-0.112546037974	0.069461141465	-0.00129840174806	0.0570527274497	0.227870120258	0.0151846241413	0.0129600716454	0.21170464595	0.00128583833531	0.0938932753984	-1.34920484731	6.00806632983	-11.49324497
16	1.45038248072	0.142381357924	-0.306956125902	1.6381638623	0.213032804579	1.03289796514	-0.0278552714717	0.132250094623	0.0298294784689	-0.122015192357	-0.0224045409789	0.0496729694568	0.0880111689769	-0.0553485600923	0.0350822041016	0.112986923337	0.00858022353523	-0.0159374651572	0.103668903244	0.00861216453112	0.0814629738379	-8.38724146402	7.36512045044	2.55346911609
17	2.58296856361	-1.23404976318	0.157606245495	2.31685546046	-0.0485923355693	2.56972777556	0.0637854056338	0.170621334881	0.0405391956377	-0.17872327413	-0.0730926259923	0.104421369449	0.120209521453	-0.145112475273	-0.00164458866667	0.119815281772	-0.0195015747778	-0.0150231919461	0.0774929799929	0.008482637495	0.111450177327	-8.55803286663	22.1874261631	-0.407109002886
18	4.67344447285	0.343748792897	2.43502210812	3.53643568326	-1.66641106614	5.2491714242	0.0577154088856	0.588852466445	-0.225262204559	-0.529131042354	0.202984009689	-0.24333230576	0.219413303202	0.133298463845	-0.282234742126	0.185395856165	-0.0272616330676	0.0738052240958	0.19265094718	-0.0208137660582	0.181113741015	2.92953004969	41.5650217501	-3.55132804447
19	2.82007861563	0.246071935411	-0.83527271864	1.78851250376	-0.216538104982	2.51433566312	0.116999683648	-0.00812486891835	0.031166390492	-0.158611905408	0.0489740332185	-0.243263962151	-0.0738030976326	0.0650203847202	-0.17269385721	0.113122816533	-0.0207636201341	0.0495240472269	0.149900392278	-0.0111447283436	0.19649812175	8.23672886284	41.6589217031	0.743122262892

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 40 through 66 )	B	G	40 - 66	38 - 64
2	2	chain 'B' and (resid 67 through 81 )	B	G	67 - 81	65 - 79
3	3	chain 'B' and (resid 82 through 129 )	B	G	82 - 129	80 - 127
4	4	chain 'B' and (resid 130 through 177 )	B	G	130 - 177	128 - 175
5	5	chain 'B' and (resid 178 through 214 )	B	G	178 - 214	176 - 204
6	6	chain 'B' and (resid 215 through 228 )	B	G	215 - 228	205 - 218
7	7	chain 'B' and (resid 229 through 261 )	B	G	229 - 261	219 - 251
8	8	chain 'C' and (resid 3 through 177 )	C	L	3 - 177	1 - 175
9	9	chain 'C' and (resid 178 through 261 )	C	L	178 - 261	176 - 259
10	10	chain 'D' and (resid 3 through 81 )	D	Q	3 - 81	1 - 79
11	11	chain 'D' and (resid 82 through 177 )	D	Q	82 - 177	80 - 175
12	12	chain 'D' and (resid 178 through 196 )	D	Q	178 - 196	176 - 194
13	13	chain 'D' and (resid 197 through 228 )	D	Q	197 - 228	195 - 218
14	14	chain 'D' and (resid 229 through 261 )	D	Q	229 - 261	219 - 251
15	15	chain 'A' and (resid 3 through 66 )	A	A	3 - 66	1 - 64
16	16	chain 'A' and (resid 67 through 215 )	A	A	67 - 215	65 - 205
17	17	chain 'A' and (resid 216 through 261 )	A	A	216 - 261	206 - 251
18	18	chain 'B' and (resid 3 through 16 )	B	G	3 - 16	1 - 14
19	19	chain 'B' and (resid 17 through 39 )	B	G	17 - 39	15 - 37

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