PDB-7wap: Mevo lectin mutant D134A

Basic information

• Entry: Database: PDB / ID: 7wap
• Title: Mevo lectin mutant D134A
• Components: Mevo lectin
• Keywords: SUGAR BINDING PROTEIN / Mevo lectin / heptamer / archeal lectin
• Function / homology: Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta / Jacalin-type lectin domain-containing protein
• Biological species: Methanococcus voltae A3 (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
• Authors: Sivaji, N. / Vijayan, M.

Funding support

India, 1items

Organization	Grant number	Country
Science and Engineering Research Board (SERB)		India

• Citation: Journal: To Be Published; Title: Mevo lectin mutant D134A; Authors: Sivaji, N. / Vijayan, M.

History

Deposition	Dec 14, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Assembly

Deposited unit

B: Mevo lectin

G: Mevo lectin

A: Mevo lectin

D: Mevo lectin

E: Mevo lectin

F: Mevo lectin

C: Mevo lectin

H: Mevo lectin

I: Mevo lectin

J: Mevo lectin

K: Mevo lectin

L: Mevo lectin

M: Mevo lectin

N: Mevo lectin

Summary:

• 220 kDa, 14 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	220,357	14
Polymers	220,357	14
Non-polymers	0	0
Water	0	0

1

B: Mevo lectin

G: Mevo lectin

A: Mevo lectin

D: Mevo lectin

E: Mevo lectin

F: Mevo lectin

C: Mevo lectin

Summary:

• defined by author
• Evidence: gel filtration
• 110 kDa, 7 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,179	7
Polymers	110,179	7
Non-polymers	0	0
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

2

H: Mevo lectin

I: Mevo lectin

J: Mevo lectin

K: Mevo lectin

L: Mevo lectin

M: Mevo lectin

N: Mevo lectin

Summary:

• defined by author
• 110 kDa, 7 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,179	7
Polymers	110,179	7
Non-polymers	0	0
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	46.810, 169.260, 160.940
Angle α, β, γ (deg.)	90.000, 91.400, 90.000
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains B G
2	2	Chains B A
3	3	Chains B D
4	4	Chains B E
5	5	Chains B F
6	6	Chains B C
7	7	Chains B H
8	8	Chains B I
9	9	Chains B J
10	10	Chains B K
11	11	Chains B L
12	12	Chains B M
13	13	Chains B N
14	14	Chains G A
15	15	Chains G D
16	16	Chains G E
17	17	Chains G F
18	18	Chains G C
19	19	Chains G H
20	20	Chains G I
21	21	Chains G J
22	22	Chains G K
23	23	Chains G L
24	24	Chains G M
25	25	Chains G N
26	26	Chains A D
27	27	Chains A E
28	28	Chains A F
29	29	Chains A C
30	30	Chains A H
31	31	Chains A I
32	32	Chains A J
33	33	Chains A K
34	34	Chains A L
35	35	Chains A M
36	36	Chains A N
37	37	Chains D E
38	38	Chains D F
39	39	Chains D C
40	40	Chains D H
41	41	Chains D I
42	42	Chains D J
43	43	Chains D K
44	44	Chains D L
45	45	Chains D M
46	46	Chains D N
47	47	Chains E F
48	48	Chains E C
49	49	Chains E H
50	50	Chains E I
51	51	Chains E J
52	52	Chains E K
53	53	Chains E L
54	54	Chains E M
55	55	Chains E N
56	56	Chains F C
57	57	Chains F H
58	58	Chains F I
59	59	Chains F J
60	60	Chains F K
61	61	Chains F L
62	62	Chains F M
63	63	Chains F N
64	64	Chains C H
65	65	Chains C I
66	66	Chains C J
67	67	Chains C K
68	68	Chains C L
69	69	Chains C M
70	70	Chains C N
71	71	Chains H I
72	72	Chains H J
73	73	Chains H K
74	74	Chains H L
75	75	Chains H M
76	76	Chains H N
77	77	Chains I J
78	78	Chains I K
79	79	Chains I L
80	80	Chains I M
81	81	Chains I N
82	82	Chains J K
83	83	Chains J L
84	84	Chains J M
85	85	Chains J N
86	86	Chains K L
87	87	Chains K M
88	88	Chains K N
89	89	Chains L M
90	90	Chains L N
91	91	Chains M N

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91

Components

#1: Protein

B G A D E F C H I J K L M N
Mevo lectin

Details:

Mass: 15739.802 Da / Num. of mol.: 14 / Mutation: D134A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus voltae A3 (archaea) / Strain: ATCC BAA-1334 / A3 / Gene: Mvol_0737 / Production host: Escherichia coli (E. coli) / References: UniProt: D7DTD6

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.89 ų/Da / Density % sol: 52.75 %
• Crystal grow: Temperature: 295 K / Method: microbatch / pH: 5.6 ; Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9799 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2020
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9799 Å / Relative weight: 1
• Reflection: Resolution: 3.1→84.63 Å / Num. obs: 118097 / % possible obs: 91.8 % / Redundancy: 2.8 % / CC_1/2: 0.97 / R_merge(I) obs: 0.148 / Net I/σ(I): 4.7
• Reflection shell: Resolution: 3.1→3.27 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14028 / CC_1/2: 0.929

Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BSB

7bsb

Resolution: 3.1→84.62 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.867 / Cross valid method: THROUGHOUT / ESU R Free: 0.541
Details: Hydrogens have been added in their riding positions

	Rfactor	Num. reflection	% reflection
Rfree	0.2748	2114	5.086 %
Rwork	0.2278	39452	-
all	0.23	-	-
obs	-	41566	91.491 %

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 43.658 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	9.741 Å2	0 Å2	-5.685 Å2
2-	-	-6.978 Å2	0 Å2
3-	-	-	-2.482 Å2

Refinement step

Cycle: LAST / Resolution: 3.1→84.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14478	0	0	0	14478

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	14738
X-RAY DIFFRACTION	r_bond_other_d	0.037	0.017	13557
X-RAY DIFFRACTION	r_angle_refined_deg	1.989	1.636	19924
X-RAY DIFFRACTION	r_angle_other_deg	2.559	1.579	31367
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.615	5	1934
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.902	24.096	586
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.738	15	2398
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.7	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	2076
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	16650
X-RAY DIFFRACTION	r_gen_planes_other	0.017	0.02	3011
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	2256
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.223	0.2	12157
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	6822
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	6185
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	122
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.036	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.405	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.453	0.2	68
X-RAY DIFFRACTION	r_mcbond_it	6.743	4.587	7784
X-RAY DIFFRACTION	r_mcbond_other	6.743	4.587	7783
X-RAY DIFFRACTION	r_mcangle_it	10.372	6.878	9702
X-RAY DIFFRACTION	r_mcangle_other	10.371	6.879	9703
X-RAY DIFFRACTION	r_scbond_it	6.48	5.014	6954
X-RAY DIFFRACTION	r_scbond_other	6.479	5.014	6955
X-RAY DIFFRACTION	r_scangle_it	10.108	7.334	10222
X-RAY DIFFRACTION	r_scangle_other	10.109	7.334	10222
X-RAY DIFFRACTION	r_lrange_it	13.41	51.619	14767
X-RAY DIFFRACTION	r_lrange_other	13.409	51.622	14768
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.1	0.05	3723
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.097	0.05	3833
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.095	0.05	4000
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.095	0.05	3932
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.09	0.05	3957
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.098	0.05	3947
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.091	0.05	4039
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.094	0.05	3689
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.106	0.05	3810
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.097	0.05	3940
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.095	0.05	3955
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.099	0.05	3929
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.144	0.05	3764
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.098	0.05	3580
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.094	0.05	3720
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.105	0.05	3667
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.1	0.05	3676
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.097	0.05	3686
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.094	0.05	3707
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.094	0.05	3721
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.103	0.05	3553
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.102	0.05	3659
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.111	0.05	3690
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.101	0.05	3665
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.135	0.05	3540
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.092	0.05	3871
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.087	0.05	3811
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.068	0.05	3867
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.088	0.05	3817
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.086	0.05	3876
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.091	0.05	3577
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.085	0.05	3878
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.103	0.05	3793
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.096	0.05	3837
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.074	0.05	3842
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.128	0.05	3724
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.092	0.05	3937
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.087	0.05	3976
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.092	0.05	3950
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.089	0.05	4003
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.085	0.05	3704
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.093	0.05	3822
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.089	0.05	3959
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.107	0.05	3966
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.086	0.05	3961
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.138	0.05	3776
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.073	0.05	3927
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.087	0.05	3932
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.094	0.05	3908
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.1	0.05	3658
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.097	0.05	3770
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.101	0.05	3840
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.071	0.05	3997
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.082	0.05	3903
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.133	0.05	3767
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.081	0.05	3957
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.078	0.05	3985
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.086	0.05	3714
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.083	0.05	3820
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.099	0.05	3888
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.086	0.05	3922
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.064	0.05	4035
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.131	0.05	3782
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.094	0.05	3934
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.094	0.05	3678
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.093	0.05	3786
X-RAY DIFFRACTION	r_ncsr_local_group_67	0.098	0.05	3875
X-RAY DIFFRACTION	r_ncsr_local_group_68	0.094	0.05	3934
X-RAY DIFFRACTION	r_ncsr_local_group_69	0.081	0.05	3937
X-RAY DIFFRACTION	r_ncsr_local_group_70	0.129	0.05	3767
X-RAY DIFFRACTION	r_ncsr_local_group_71	0.081	0.05	3721
X-RAY DIFFRACTION	r_ncsr_local_group_72	0.096	0.05	3838
X-RAY DIFFRACTION	r_ncsr_local_group_73	0.094	0.05	3936
X-RAY DIFFRACTION	r_ncsr_local_group_74	0.103	0.05	3957
X-RAY DIFFRACTION	r_ncsr_local_group_75	0.085	0.05	3964
X-RAY DIFFRACTION	r_ncsr_local_group_76	0.136	0.05	3795
X-RAY DIFFRACTION	r_ncsr_local_group_77	0.1	0.05	3531
X-RAY DIFFRACTION	r_ncsr_local_group_78	0.097	0.05	3627
X-RAY DIFFRACTION	r_ncsr_local_group_79	0.102	0.05	3662
X-RAY DIFFRACTION	r_ncsr_local_group_80	0.091	0.05	3689
X-RAY DIFFRACTION	r_ncsr_local_group_81	0.138	0.05	3534
X-RAY DIFFRACTION	r_ncsr_local_group_82	0.09	0.05	3850
X-RAY DIFFRACTION	r_ncsr_local_group_83	0.104	0.05	3786
X-RAY DIFFRACTION	r_ncsr_local_group_84	0.088	0.05	3798
X-RAY DIFFRACTION	r_ncsr_local_group_85	0.125	0.05	3717
X-RAY DIFFRACTION	r_ncsr_local_group_86	0.106	0.05	3867
X-RAY DIFFRACTION	r_ncsr_local_group_87	0.101	0.05	3868
X-RAY DIFFRACTION	r_ncsr_local_group_88	0.137	0.05	3760
X-RAY DIFFRACTION	r_ncsr_local_group_89	0.092	0.05	3918
X-RAY DIFFRACTION	r_ncsr_local_group_90	0.14	0.05	3795
X-RAY DIFFRACTION	r_ncsr_local_group_91	0.127	0.05	3766

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
3.1-3.181	0.358	110	0.341	2478	X-RAY DIFFRACTION	77.7177
3.181-3.268	0.381	149	0.322	2530	X-RAY DIFFRACTION	81.9767
3.268-3.362	0.299	158	0.301	2572	X-RAY DIFFRACTION	85.1528
3.362-3.466	0.278	136	0.24	2515	X-RAY DIFFRACTION	87.2326
3.466-3.579	0.292	146	0.262	2551	X-RAY DIFFRACTION	88.6879
3.579-3.705	0.272	140	0.245	2454	X-RAY DIFFRACTION	90.6359
3.705-3.845	0.343	124	0.239	2506	X-RAY DIFFRACTION	93.7611
3.845-4.002	0.285	175	0.224	2354	X-RAY DIFFRACTION	94.6836
4.002-4.179	0.249	151	0.207	2335	X-RAY DIFFRACTION	96.4688
4.179-4.383	0.245	96	0.183	2299	X-RAY DIFFRACTION	96.8851
4.383-4.62	0.207	117	0.181	2164	X-RAY DIFFRACTION	96.2854
4.62-4.9	0.201	98	0.16	2015	X-RAY DIFFRACTION	96.484
4.9-5.238	0.204	128	0.168	1897	X-RAY DIFFRACTION	95.8353
5.238-5.657	0.319	71	0.22	1796	X-RAY DIFFRACTION	97.0374
5.657-6.197	0.32	65	0.233	1662	X-RAY DIFFRACTION	96.8592
6.197-6.927	0.25	61	0.208	1519	X-RAY DIFFRACTION	96.518
6.927-7.996	0.251	62	0.187	1342	X-RAY DIFFRACTION	96.4286
7.996-9.787	0.33	53	0.23	1112	X-RAY DIFFRACTION	96.9218
9.787-13.815	0.198	27	0.225	878	X-RAY DIFFRACTION	95.9703
13.815-84.6	0.32	47	0.35	473	X-RAY DIFFRACTION	95.7643