PDB-4gop: Structure and Conformational Change of a Replication Protein A He...

ID or keywords:

Entry

Database: PDB / ID: 4gop

Title

Structure and Conformational Change of a Replication Protein A Heterotrimer Bound to ssDNA

Components

(Putative uncharacterized protein) x 3
DNA (25-MER)

Keywords

DNA BINDING PROTEIN/DNA / OB fold /

ssDNA binding / DNA BINDING PROTEIN-DNA complex

Function / homology

Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) /

Beta Barrel / Mainly Beta /

DNA / DNA (> 10) / : / : / :

Function and homology information

Biological species

Ustilago maydis (fungus)
synthetic (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Pavletich, N.P. / Jie, F.

Citation

Journal: Genes Dev. / Year: 2012
Title: Structure and conformational change of a replication protein A heterotrimer bound to ssDNA.
Authors: Fan, J. / Pavletich, N.P.

History

Deposition	Aug 20, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gop.cif.gz	580.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4gop.ent.gz	494.1 KB	Display	PDB format
PDBx/mmJSON format	4gop.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/go/4gop ftp://data.pdbj.org/pub/pdb/validation_reports/go/4gop	HTTPS FTP

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Related structure data

Similar structure data	4gnx-1 4gnx-2 4a7p-d 5mbt-d 1d5a-d 3ks9-d 3ohu-d 3mwy-d 4z1i-1 1ek2-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

X: Putative uncharacterized protein

Y: Putative uncharacterized protein

Z: Putative uncharacterized protein

K: DNA (25-MER)

L: DNA (25-MER)

hetero molecules

174 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

K: DNA (25-MER)

hetero molecules

defined by author&software
87 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

X: Putative uncharacterized protein

Y: Putative uncharacterized protein

Z: Putative uncharacterized protein

L: DNA (25-MER)

hetero molecules

defined by author&software
87 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	184.100, 93.800, 120.500
Angle α, β, γ (deg.)	90.000, 110.900, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	3 - 67
2	1	1	2	X	3 - 67
1	2	1	2	A	74 - 79
2	2	1	2	X	74 - 79
1	1	2	2	A	92 - 112
2	1	2	2	X	92 - 112
1	1	3	2	B	46 - 60
2	1	3	2	Y	46 - 60
1	2	3	2	B	69 - 112
2	2	3	2	Y	69 - 112
1	1	4	2	B	153 - 175
2	1	4	2	Y	153 - 175
1	1	5	2	C	182 - 208
2	1	5	2	Z	182 - 208
1	2	5	2	C	219 - 297
2	2	5	2	Z	219 - 297
1	1	6	2	C	298 - 327
2	1	6	2	Z	298 - 327
1	2	6	2	C	341 - 431
2	2	6	2	Z	341 - 431
1	1	7	2	C	441 - 447
2	1	7	2	Z	441 - 447
1	1	8	2	C	448 - 486
2	1	8	2	Z	448 - 486
1	2	8	2	C	523 - 586
2	2	8	2	Z	523 - 586
1	3	8	2	C	596 - 606
2	3	8	2	Z	596 - 606
1	1	9	2	C	487 - 522
2	1	9	2	Z	487 - 522
1	2	9	2	C	701
2	2	9	2	Z	701
1	1	10	2	C	607 - 623
2	1	10	2	Z	607 - 623

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	Putative uncharacterized protein Mass: 12175.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (fungus) / Strain: 521 / FGSC 9021 / Gene: UM04165.1 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4P6U8
#2: Protein	Putative uncharacterized protein Mass: 15248.052 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (fungus) / Strain: 521 / FGSC 9021 / Gene: UM02579.1 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4PBD4
#3: Protein	Putative uncharacterized protein Mass: 49837.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (fungus) / Strain: 521 / FGSC 9021 / Gene: UM05156.1 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4P407
#4: DNA chain	DNA (25-MER) Mass: 9689.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.99 %

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 1.04022 Å

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.04022 Å / Relative weight: 1

Reflection

Resolution: 3.1→35 Å / Num. all: 35186 / Num. obs: 32477 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / R_merge(I) obs: 0.103 / Χ²: 1.294 / Net I/σ(I): 7.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3.1-3.21	2.7	0.512	3311	1.12	1	94.5
3.21-3.34	2.7	0.368	3309	1.152	1	94.8
3.34-3.49	2.7	0.263	3275	1.231	1	93.8
3.49-3.67	2.7	0.19	3287	1.233	1	93.3
3.67-3.9	2.7	0.143	3245	1.238	1	93.2
3.9-4.21	2.7	0.099	3241	1.237	1	92.5
4.21-4.63	2.7	0.074	3235	1.358	1	92.2
4.63-5.3	2.8	0.067	3211	1.304	1	91
5.3-6.66	2.8	0.072	3225	1.428	1	90.6
6.66-35	2.8	0.043	3138	1.637	1	86.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
ADSC	Quantum	data collection
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / Cor.coef. F_o:F_c: 0.885 / Cor.coef. F_o:F_c free: 0.831 / Occupancy max: 1 / Occupancy min: 1 / SU B: 64.323 / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.6 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.286	1513	5 %	RANDOM
R_work	0.2418	-	-	-
all	0.2441	35186	-	-
obs	0.2441	30014	85.54 %	-

Solvent computation

Ion probe radii: 1 Å / Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso max: 219.4 Å² / B_iso mean: 88.629 Å² / B_iso min: 16.77 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.06 Å²	0 Å²	2.38 Å²
2-	-	-6.78 Å²	0 Å²
3-	-	-	6.42 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10448	900	2	0	11350

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	11623
X-RAY DIFFRACTION	r_angle_refined_deg	1.363	1.893	15908
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.895	5	1314
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.357	24.44	536
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.178	15	1826
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.809	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1745
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	8566

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	68	TIGHT POSITIONAL	0.03	0.05
1	A	245	MEDIUM POSITIONAL	0.04	0.5
1	A	284	TIGHT THERMAL	3.04	99
1	A	245	MEDIUM THERMAL	4.08	99
2	A	77	MEDIUM POSITIONAL	0.04	0.5
2	A	84	TIGHT THERMAL	1.89	99
2	A	77	MEDIUM THERMAL	4.61	99
3	B	224	MEDIUM POSITIONAL	0.04	0.5
3	B	236	TIGHT THERMAL	3.14	99
3	B	224	MEDIUM THERMAL	3.91	99
4	B	103	MEDIUM POSITIONAL	0.04	0.5
4	B	92	TIGHT THERMAL	2.53	99
4	B	103	MEDIUM THERMAL	4.55	99
5	C	437	MEDIUM POSITIONAL	0.04	0.5
5	C	424	TIGHT THERMAL	2.78	99
5	C	437	MEDIUM THERMAL	3.9	99
6	C	465	MEDIUM POSITIONAL	0.03	0.5
6	C	484	TIGHT THERMAL	10.59	99
6	C	465	MEDIUM THERMAL	12.54	99
7	C	6	MEDIUM POSITIONAL	0.03	0.5
7	C	28	TIGHT THERMAL	32.73	99
7	C	6	MEDIUM THERMAL	31.04	99
8	C	455	MEDIUM POSITIONAL	0.04	0.5
8	C	456	TIGHT THERMAL	3.9	99
8	C	455	MEDIUM THERMAL	5	99
9	C	152	MEDIUM POSITIONAL	0.51	0.5
9	C	144	TIGHT THERMAL	12.82	99
9	C	152	MEDIUM THERMAL	12.51	99
10	C	63	MEDIUM POSITIONAL	0.04	0.5
10	C	68	TIGHT THERMAL	3.41	99
10	C	63	MEDIUM THERMAL	4.91	99

LS refinement shell

Resolution: 3.1→3.179 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	87	-
R_work	0.311	1715	-
all	-	1802	-
obs	-	-	71.88 %

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	5.7917	3.6208	-0.2109	4.129	-0.968	4.8858	-0.2247	-0.2825	0.1854	0.1953	-0.1868	-0.6321	-0.2549	0.4782	0.4115	0.1095	0.0204	-0.1286	0.0761	0.0123	0.3142	10.24	23.913	-44.754
2	6.4889	1.66	-0.0039	6.4612	0.2952	3.658	0.1233	-0.5059	0.542	0.7524	-0.1085	0.7435	-0.596	-0.7114	-0.0148	0.2486	0.1101	0.0678	0.2212	-0.0001	0.136	-12.122	24.934	-35.552
3	5.7543	0.3494	0.0104	9.598	-1.8174	5.2516	-0.1621	-0.0251	-0.2874	-0.0423	0.4536	0.5912	0.1148	-0.7418	-0.2915	0.0981	-0.042	0.031	0.1182	0.0356	0.1468	-1.283	-16.418	-54.857
4	7.0432	-0.3967	-2.3981	3.1996	1.3079	3.2238	-0.1142	-0.3271	0.0515	0.1295	-0.1942	0.6694	-0.0922	-0.2795	0.3083	0.6011	0.2181	-0.1048	0.7758	-0.079	0.3494	4.368	-21.381	-28.08
5	1.7799	1.5706	-0.3072	4.6132	0.8755	6.1815	0.1809	-0.7865	-0.0607	1.0456	-0.2915	0.391	0.0908	-0.3791	0.1106	0.4531	0.0402	-0.038	0.532	0.0645	0.2165	-11.683	8.843	-17.089
6	0.9878	1.3722	-3.4823	2.0931	-5.4051	14.4681	0.2996	-0.4058	-0.2376	0.6237	-0.0769	-0.151	-1.1446	-0.248	-0.2227	1.2592	0.0074	-0.2523	1.8152	0.5417	1.0218	-11.768	11.847	9.493
7	7.0644	-2.4226	-0.4301	6.4129	1.0327	3.6648	-0.0968	0.3752	-0.232	-0.2312	-0.24	-0.4396	0.0345	0.3812	0.3369	0.0201	0.0017	0.0502	0.0829	0.0263	0.1456	9.382	7.481	-66.664
8	3.8315	-1.5845	-0.2742	6.1994	1.4723	2.8915	0.0076	0.3578	-0.4018	-0.5192	-0.1388	0.6481	0.3515	-0.4823	0.1311	0.1621	-0.078	-0.0164	0.1708	-0.0094	0.1307	-12.821	7.261	-73.704
9	4.7396	0.0828	0.1347	7.6453	-1.8085	8.5261	-0.0798	-0.1418	0.2594	0.3234	0.3693	0.5598	-0.0841	-0.9116	-0.2895	0.09	0.0366	0.0041	0.1097	0.0298	0.1573	-1.323	47.77	-55.701
10	4.679	1.0215	0.0599	3.5028	0.1755	3.7934	-0.1161	0.6696	-0.1361	-0.269	0.2747	0.4363	0.0546	-0.3753	-0.1587	0.5161	-0.096	-0.0439	0.598	0.1042	0.3122	1.498	52.955	-80.992
11	0.6535	-0.7539	-0.8558	4.4891	-0.9271	4.634	0.0756	0.616	-0.0678	-0.9268	-0.2264	0.7985	0.0067	-0.6076	0.1508	0.4332	-0.0785	-0.1247	0.7607	0.0867	0.3515	-15.142	22.138	-91.956
12	18.1302	0.1698	2.5006	7.1891	1.5237	14.9058	0.2091	0.8739	0.7684	-0.909	-0.6325	-0.3762	0.4517	-0.0084	0.4234	1.0732	0.0145	-0.1336	1.212	-0.0704	0.2299	-19.032	18.504	-118.621

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 112
2	X-RAY DIFFRACTION	2	B	46 - 175
3	X-RAY DIFFRACTION	2	K	21 - 25
4	X-RAY DIFFRACTION	3	C	182 - 297
5	X-RAY DIFFRACTION	3	K	1 - 4
6	X-RAY DIFFRACTION	4	C	298 - 447
7	X-RAY DIFFRACTION	4	K	5 - 9
8	X-RAY DIFFRACTION	5	C	448 - 487
9	X-RAY DIFFRACTION	5	C	522 - 623
10	X-RAY DIFFRACTION	5	K	10 - 20
11	X-RAY DIFFRACTION	6	C	488 - 521
12	X-RAY DIFFRACTION	6	C	701
13	X-RAY DIFFRACTION	7	X	1 - 112
14	X-RAY DIFFRACTION	8	Y	46 - 175
15	X-RAY DIFFRACTION	8	L	21
16	X-RAY DIFFRACTION	9	Z	182 - 297
17	X-RAY DIFFRACTION	9	L	1 - 4
18	X-RAY DIFFRACTION	10	Z	298 - 422
19	X-RAY DIFFRACTION	10	L	5 - 9
20	X-RAY DIFFRACTION	11	Z	448 - 487
21	X-RAY DIFFRACTION	11	Z	522 - 623
22	X-RAY DIFFRACTION	11	L	13 - 18
23	X-RAY DIFFRACTION	12	Z	488 - 521
24	X-RAY DIFFRACTION	12	Z	701

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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