PDB-7rck: Crystal Structure of PMS2 with Substrate

ID or keywords:

Entry

Database: PDB / ID: 7rck

Title

Crystal Structure of PMS2 with Substrate

Components

Mismatch repair endonuclease PMS2

Keywords

HYDROLASE / Mismatch Repair / Variant of Uncertain Significance / ATPase Domain / DNA Repair Enzyme

Function / homology

Function and homology information

single base insertion or deletion binding / Defective Mismatch Repair Associated With MLH1 / Defective Mismatch Repair Associated With PMS2 / MutLalpha complex / somatic recombination of immunoglobulin gene segments / positive regulation of isotype switching to IgA isotypes / positive regulation of isotype switching to IgG isotypes / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / ATP-dependent DNA damage sensor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

D'Arcy, B.M. / Prakash, A.

Citation

Journal: Mol Genet Genomic Med / Year: 2022
Title: PMS2 variant results in loss of ATPase activity without compromising mismatch repair.
Authors: D'Arcy, B.M. / Arrington, J. / Weisman, J. / McClellan, S.B. / Yang, Z. / Deivanayagam, C. / Blount, J. / Prakash, A.

History

Deposition	Jul 7, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 30, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Oct 25, 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	7rck.cif.gz	296.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7rck.ent.gz	197.9 KB	Display	PDB format
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Validation report

Summary document	7rck_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	7rck_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7rck_validation.xml.gz	26.5 KB	Display
Data in CIF	7rck_validation.cif.gz	37.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rc/7rck ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rck	HTTPS FTP

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Related structure data

Related structure data	7rcbC 7rciC 1h7sS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7rcb-d 1h7s-d 7rci-d 6mfq-d 1ea6-d 2wv0-3 3r9u-2 6a4j-d Search similar-shape structures by Omokage search (details) 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	#150 - Jun 2012 Sliding Clamps similarity (2) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Mismatch repair endonuclease PMS2

B: Mismatch repair endonuclease PMS2

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	74.684, 75.385, 135.313
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	Details
d_1	ens_1	(chain "A" and (resid 33 through 58 or (resid 59...
d_2	ens_1	(chain "B" and (resid 33 through 80 or (resid 81...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	LEU	GLU	A	1 - 53
d_1	2	ens_1	ALA	TYR	A	57 - 202
d_1	3	ens_1	ALA	THR	A	209 - 224
d_1	4	ens_1	GLY	SER	A	226 - 276
d_1	5	ens_1	GLN	ASP	A	285 - 303
d_2	1	ens_1	LEU	THR	B	2 - 216
d_2	2	ens_1	GLY	ASP	B	218 - 287

NCS oper: (Code: givenMatrix: (-0.0100245310115, 0.999360484378, -0.0343239135571), (0.999033866038, 0.00854063579678, -0.0431090715356), (-0.0427883545661, -0.034722900283, -0.998480584142)Vector: - ...

#1: Protein	Mismatch repair endonuclease PMS2 / DNA mismatch repair protein PMS2 / PMS1 protein homolog 2 Mass: 40513.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PMS2, PMSL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3 pLysS) References: UniProt: P54278, Hydrolases; Acting on ester bonds
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H₂O
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: 2.35 Å³/Da / Density % sol: 47.67 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03317 Å / Relative weight: 1
Reflection	Resolution: 2.04→38.71 Å / Num. obs: 49151 / % possible obs: 99.51 % / Redundancy: 6.2 % / B_iso Wilson estimate: 37.5 Å² / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.06932 / R_pim(I) all: 0.03014 / R_rim(I) all: 0.07579 / Χ²: 1 / Net I/σ(I): 12.59
Reflection shell	Resolution: 2.04→2.113 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.5479 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 4825 / CC_1/2: 0.844 / CC star: 0.957 / R_pim(I) all: 0.2504 / R_rim(I) all: 0.6044 / Χ²: 1 / % possible all: 99.32

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Processing

Software

Name	Version	Classification
SAINT		data reduction
SADABS		data scaling
PHASER		phasing
PHENIX	V1.19	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1H7S

1h7s

Resolution: 2.04→38.71 Å / SU ML: 0.2128 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2344	4792	9.75 %
R_work	0.2132	44354	-
obs	0.2152	49146	99.53 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→38.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4327	0	64	344	4735

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0017	4471
X-RAY DIFFRACTION	f_angle_d	0.4644	6084
X-RAY DIFFRACTION	f_chiral_restr	0.0409	716
X-RAY DIFFRACTION	f_plane_restr	0.0032	783
X-RAY DIFFRACTION	f_dihedral_angle_d	13.8541	1556

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 1.03522866106 Å

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 (%)
2.04-2.06	0.3036	155	0.2957	1431	X-RAY DIFFRACTION	98.27
2.06-2.09	0.3407	149	0.2814	1470	X-RAY DIFFRACTION	99.75
2.09-2.11	0.3431	146	0.267	1473	X-RAY DIFFRACTION	99.94
2.11-2.14	0.2703	144	0.2729	1465	X-RAY DIFFRACTION	99.88
2.14-2.17	0.2567	144	0.2654	1473	X-RAY DIFFRACTION	99.94
2.17-2.2	0.305	159	0.2488	1479	X-RAY DIFFRACTION	99.7
2.2-2.23	0.2466	167	0.247	1451	X-RAY DIFFRACTION	99.94
2.23-2.26	0.2998	144	0.2571	1481	X-RAY DIFFRACTION	99.51
2.26-2.3	0.2545	160	0.2495	1438	X-RAY DIFFRACTION	99.69
2.3-2.34	0.3044	168	0.2499	1477	X-RAY DIFFRACTION	99.88
2.34-2.38	0.2671	165	0.2478	1428	X-RAY DIFFRACTION	99.01
2.38-2.42	0.278	165	0.2466	1495	X-RAY DIFFRACTION	99.88
2.42-2.47	0.2866	154	0.2384	1453	X-RAY DIFFRACTION	99.32
2.47-2.52	0.2352	170	0.2421	1450	X-RAY DIFFRACTION	100
2.52-2.57	0.2502	167	0.2354	1470	X-RAY DIFFRACTION	99.57
2.57-2.63	0.2691	160	0.2338	1450	X-RAY DIFFRACTION	99.2
2.63-2.7	0.2297	172	0.239	1460	X-RAY DIFFRACTION	99.21
2.7-2.77	0.2484	148	0.2472	1490	X-RAY DIFFRACTION	99.76
2.77-2.85	0.2689	209	0.2355	1417	X-RAY DIFFRACTION	99.94
2.85-2.94	0.235	164	0.22	1473	X-RAY DIFFRACTION	99.7
2.94-3.05	0.2421	147	0.2139	1495	X-RAY DIFFRACTION	99.88
3.05-3.17	0.2235	156	0.2164	1479	X-RAY DIFFRACTION	99.45
3.17-3.31	0.2095	170	0.2	1490	X-RAY DIFFRACTION	99.58
3.31-3.49	0.237	125	0.1926	1498	X-RAY DIFFRACTION	98.9
3.49-3.71	0.2173	162	0.1973	1491	X-RAY DIFFRACTION	99.64
3.71-3.99	0.2019	152	0.1935	1519	X-RAY DIFFRACTION	99.29
3.99-4.39	0.2275	120	0.1692	1563	X-RAY DIFFRACTION	100
4.39-5.03	0.1754	165	0.1707	1521	X-RAY DIFFRACTION	99.94
5.03-6.33	0.2698	179	0.2132	1514	X-RAY DIFFRACTION	99.3
6.33-38.71	0.2093	206	0.2177	1560	X-RAY DIFFRACTION	98.06

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	2.62215695271	0.874034840687	-0.722515076226	5.46714409747	-1.59951233205	3.18150900131	-0.0165602873675	-0.0905835457051	-0.0586262751557	0.228165112576	0.0258689296552	0.108451218966	-0.14048813535	0.0103626192069	-0.00947341787784	0.199915649599	0.00871854447547	0.00357227334401	0.261738981352	0.00895252000501	0.274582553719	1.05286722094	8.83521517357	-39.9118138208
2	4.96373269553	0.389716159745	-0.0167289114658	7.54893165189	-2.11955650608	6.26174113425	-0.27715172911	-0.10996385589	0.588578083352	0.548980148372	-0.018849030406	-0.666102348132	-0.884525916353	0.367780057025	0.296371051088	0.428360603456	-0.00456318231872	-0.104798004311	0.405167564886	0.0141592156454	0.423543607066	12.2809135472	8.00892549924	-33.4967326644
3	3.26958199951	-0.652369198689	0.297095407717	5.45956847599	-2.0807678961	3.72321770661	-0.0774909215357	0.060753107914	0.0317832099444	-0.248483633397	-0.112782744619	-0.519489532754	-0.138862638558	0.312285173279	0.216853408461	0.269991306252	-0.0160584810874	0.0177623915791	0.336106449868	-0.0027804561617	0.3632169308	13.7501645465	7.18357208998	-44.4565270951
4	1.8815058355	-1.92524581498	0.665706487299	4.35481849773	-1.15360840387	0.534970782409	-0.261630513249	-0.313469411947	-0.462120667001	0.393841532869	0.355679574819	0.267598073275	0.166994132688	-0.0942378849837	-0.0889711164724	0.34105067599	-0.00421068610928	0.063077633767	0.253409167997	0.0491502543939	0.308306190304	-5.02898811311	-0.547718424464	-32.9891691554
5	4.71017296433	-3.15875919424	-1.64911504398	5.10493233153	1.47003793731	4.33578937051	0.105387421773	0.337271275791	-0.112073175267	-0.273192666973	-0.182867004345	0.205821320357	0.0247984217722	-0.261892959902	0.0664226141617	0.21292861611	-0.0278054094186	-0.0255570114287	0.259755002454	0.0241597839814	0.245516071562	-11.0753505333	11.6206128232	-45.1136975596
6	3.35434690764	-0.748645354636	-0.624479343526	5.53360931322	1.54171882379	0.601952791686	0.277186131459	-0.0923450154237	0.225695870679	0.652904293651	-0.356447331735	0.764699903636	0.27376673297	-0.703188222691	0.0283249157574	0.308726609936	-0.059327564014	0.130666836842	0.347400434777	0.0263443575582	0.457290517223	-25.0801269117	25.8778980643	-26.8741124071
7	3.56093210022	-0.488131855962	-1.36422989752	2.29397298601	-1.28497686855	1.51580728977	-0.0216690324476	-0.337373028464	-0.300826129573	0.48171204878	-0.137982941122	0.306132155312	0.324702186409	-0.180486888171	0.0641465985954	0.343662496103	-0.0632498396476	0.105533707189	0.359548561739	0.00338597256661	0.379144225274	-22.4025438288	23.1999993855	-24.1425713013
8	4.12195478014	-0.725010778726	-1.29970720232	3.5075438287	1.19871961679	3.72165812735	-0.01143606665	-0.377534767591	-0.0362199447366	0.925490680083	-0.0773535698141	0.472835449104	0.703856733886	-0.201246913388	0.071804031564	0.468227838038	-0.0314145417577	0.111973771657	0.351766378438	0.0241649799762	0.336664268302	-18.2377792263	18.7200341256	-24.4951849024
9	4.66495837565	1.01129679229	-0.551600206107	5.49668372421	2.41518291852	5.37253446966	0.00705775751517	-1.11909797703	-0.450221355572	1.02285377443	0.0164928535307	0.576412813746	0.410815481553	-0.312676917318	0.0123680984499	0.494834653362	-0.0325128812002	0.173164698381	0.360607384731	0.0172319338042	0.360392881538	-19.4730835048	25.1627156386	-19.2176911148
10	6.71105884656	0.859386127776	-0.313778643049	4.78534868107	0.524410671031	3.93517222256	-0.116465722491	0.173154787715	0.257014127805	-0.170282285817	0.172011471451	-0.212379306365	-0.246433012289	-0.000978847028239	-0.0365303255577	0.290448605559	-0.0175965987604	-0.0340266656974	0.267818065279	0.0142436368371	0.251073663687	-7.09705609574	20.0332814845	-61.5381451709
11	6.48778044011	0.989238213325	2.42752282158	3.03568912722	0.960836306481	4.01673049235	-0.488221976494	0.966364124116	0.874542096243	-0.301427075262	0.238728719074	-0.108092126953	-0.924016375242	0.160295744972	0.242445208771	0.500730340575	-0.0782153757411	-0.136101462139	0.38997163063	0.110496371898	0.524490311401	-8.62745928924	32.6469291115	-67.4650769367
12	4.70646964605	-0.567895247678	0.593730029747	2.88915663591	-0.524641792257	2.57379982529	-0.245833532227	0.0347534927263	0.422889369854	-0.0125904490182	0.125583257489	-0.0975687257458	-0.342619945682	-0.0122368089731	0.121832926595	0.328066212219	0.0174061791179	-0.0634058102352	0.269799420163	0.00700409668763	0.251365889113	-13.6982239449	28.3413468468	-60.9163135781
13	7.81720186969	-1.67000474891	0.0181830874356	2.14757646842	-0.595459990433	1.45029517089	-0.106276737078	0.704407858486	-0.420325890847	-0.497362487311	-0.00379782405022	0.216456021201	-0.0625554370723	-0.0316207472094	0.11507649633	0.274777043106	-0.0380971376213	-0.0353969137574	0.316531164024	-0.0470994523129	0.30137649873	-8.95156005168	8.54947184496	-65.6399645028
14	5.45713826168	-1.32326008727	-2.38910985144	3.08218421016	0.137592255595	2.9822844118	-0.164748128417	-0.146439797572	-0.194758989419	-0.0230295342584	0.0571143764796	-0.0694786562533	0.112435792695	0.128007618422	0.11212771184	0.263749881572	-0.0392396326713	-0.00849241063602	0.258043527214	0.00939577884556	0.233708921062	-4.55469159308	8.56488502679	-55.3610562878
15	2.39986645297	-0.957709330937	0.879673101407	2.53397953638	1.34377133336	1.6712137253	-0.485763206169	0.550995102045	-0.651544820376	-0.52825958295	0.168044890364	-0.0335196324101	0.573083864474	-0.41804067712	0.210472647429	0.578196555364	-0.202254697688	0.190408032601	0.453088274844	-0.142519926027	0.464492336381	6.86758943171	-4.87398502729	-72.7438240133
16	3.20562064611	0.279517063476	-0.8227090895	4.92836496262	1.32363911948	1.64603278334	-0.35080316745	0.971988357449	-0.536664914887	-0.733547823216	0.150524207779	0.120231136219	0.639589718299	-0.578602770311	0.158027865132	0.559641758055	-0.224476071108	0.0376927556796	0.628022981711	-0.123367254992	0.379390720075	0.923588076088	-0.504577397386	-76.3511533927
17	1.83103113038	-1.00358683471	-0.291106097738	2.18114212051	2.35370689626	3.00598142678	-0.807807128877	1.00022330976	-0.719672927555	-0.893296367254	0.477681618542	-0.174983027996	0.492445760471	-0.557267021438	0.327829975763	0.689500864413	-0.238093180655	0.165411194737	0.609397677627	-0.160495417398	0.431650832878	6.66619435414	-3.16192235678	-77.4728158748

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 'A' and (resid 33 through 76 )	A	A	33 - 76	1 - 44
2	2	chain 'A' and (resid 77 through 117 )	A	A	77 - 117	45 - 64
3	3	chain 'A' and (resid 118 through 160 )	A	A	118 - 160	65 - 107
4	4	chain 'A' and (resid 161 through 194 )	A	A	161 - 194	108 - 141
5	5	chain 'A' and (resid 195 through 231 )	A	A	195 - 231	142 - 178
6	6	chain 'A' and (resid 232 through 254 )	A	A	232 - 254	179 - 201
7	7	chain 'A' and (resid 255 through 287 )	A	A	255 - 287	202 - 234
8	8	chain 'A' and (resid 288 through 331 )	A	A	288 - 331	235 - 278
9	9	chain 'A' and (resid 332 through 364 )	A	A	332 - 364	279 - 303
10	10	chain 'B' and (resid 32 through 76 )	B	B	32 - 76	1 - 45
11	11	chain 'B' and (resid 77 through 117 )	B	B	77 - 117	46 - 62
12	12	chain 'B' and (resid 118 through 176 )	B	B	118 - 176	63 - 121
13	13	chain 'B' and (resid 177 through 194 )	B	B	177 - 194	122 - 139
14	14	chain 'B' and (resid 195 through 231 )	B	B	195 - 231	140 - 176
15	15	chain 'B' and (resid 232 through 287 )	B	B	232 - 287	177 - 226
16	16	chain 'B' and (resid 288 through 313 )	B	B	288 - 313	227 - 252
17	17	chain 'B' and (resid 314 through 364 )	B	B	314 - 364	253 - 287

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