1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Zheng, D.
Tashiro, M.
Aramini, J.M.
Montelione, G.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Protein Sci.
PRCIEI
0795
0961-8368
13
549
554
10.1110/ps.03351704
14718654
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
2004
US
Biochemistry
BICHAW
0033
0006-2960
35
22
31
10.1021/bi9512814
The Mechanism of Binding Staphylococcal Protein a to Immunoglobin G Does not Involve Helix Unwinding
1996
UK
Curr.Opin.Struct.Biol.
COSBEF
0801
0959-440X
5
471
481
10.1016/0959-440X(95)80031-X
Structures of Bacterial Immunoglobulin-Binding Domains and Their Complexes with Immunoglobulin
1995
US
Biochemistry
BICHAW
0033
0006-2960
32
7839
7845
An Improved Strategy for Determining Resonance Assignments for Isotopically Enriched Proteins and its Application to an Engineered Domain of Staphylococcal Protein A
1993
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
272
573
590
10.1006/jmbi.1997.1265
High Resolution Solution NMR Structure of the Z Domain of Staphylococcal Protein A
1997
10.2210/pdb1q2n/pdb
pdb_00001q2n
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
6648.316
IMMUNOGLOBULIN G BINDING PROTEIN A
residues 212-269
1
man
polymer
IGG binding protein A
no
no
VDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPK
VDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPK
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Staphylococcus
Escherichia
sample
CELL WALL
1280
Staphylococcus aureus
562
Escherichia coli
RV308
PLASMID
PDHZ
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2003-08-12
1
1
2008-04-29
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2003-07-25
REL
REL
NMR EXPERIMENTS CONDUCTED: 2D PFG-[15N]HSQC, 3D PFG-HNCO, 3D PFG-(HA)CA(CO)NH, 3D PFG-HA(CA)(CO)NH, 3D PFG-HA(CA)NH, 3D PFG-CBCANH, 3D PFG-CBCA(CO)NH, 3D PFG- (HA)CANH, 3D PFG-HN(CA)CO, 3D PFG-HCCNH-TOCSY, 3D PFG-HCC (CO)NH-TOCSY, 2D [15N]HSQC-IPAP, 3D Ca-coupled HNCO
structures with the lowest energy
100
10
20 mM NH4OAc
6.50
1
atm
303.00
K
THE STRUCTURES ARE BASED ON A TOTAL OF 769 CONFORMATIONAL RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 536; INTRA-RESIDUE [I=J] = 224; SEQUENTIAL [(I-J)=1] = 142; MEDIUM RANGE [1<(I-J)<5] 105; LONG RANGE [(I-J)>=5] = 65; NUMBER OF DISTANCE CONSTRAINTS RESIDUE = 9.2; DIHEDRAL-ANGLE CONSTRAINTS = 107 RESIDUAL DIPOLAR COUPLING CONSTRAINTS = 126 (34 N-H, 43 HA-CA, 4 TOTAL NUMBER OF CONSTRAINTS PER RESIDUE = 13.3; NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 3.3; NUMBER OF STRUCTURES COMPUTED = 100; NUMBER OF STRUCTURES USED = 10. AVERAGE RESIDUAL CONSTRAINT VIOLATIONS: DISTANCE VIOLATIONS 0.1-0.2 ANG = 7.7, 0. 0.8, >0.5 ANG = 0.3. AVERAGE R.M.S. DISTANCE VIOLATION = 0.03 AN AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 0; RMSD VALUES: BACKBONE ATOMS (N,C,C') = 1.2 ANG; BACKBONE ATOMS(N,C,C') OF ORDERED RESIDUES = 0.4 ANG; ALL HEAVY = 1.7 ANG; ALL HEAVY ATOMS OF ORDERED RESIDUES = 1.0 ANG. PROCHECK USING ORDERED RESIDUES (5-36,39-57): MOST FAVORED REGIONS = 91.4%; ADDITIONAL ALLOWED REGIONS = 8.4%; GENEROUSLY ALLOWED REGIONS = 0.2%; DISALLOWED REGIONS = 0%.
SIMULATED ANNEALING WITH RESTRAINED MOLECULAR DYNAMICS, PROTOCAL USED: ANNEAL.INP
1
lowest energy
1mM Z domain U-15N,13C; 20mM NH4OAc buffer; 95% H2O, 5% D2O.
95% H2O/5% D2O
BRUNGER, A.T.
refinement
CNS
1.0
BRUNGER, A.T.
structure solution
CNS
1.0
500
Varian
MODIFIED UNITY 500
VAL
1
n
1
VAL
1
A
ASP
2
n
2
ASP
2
A
ASN
3
n
3
ASN
3
A
LYS
4
n
4
LYS
4
A
PHE
5
n
5
PHE
5
A
ASN
6
n
6
ASN
6
A
LYS
7
n
7
LYS
7
A
GLU
8
n
8
GLU
8
A
GLN
9
n
9
GLN
9
A
GLN
10
n
10
GLN
10
A
ASN
11
n
11
ASN
11
A
ALA
12
n
12
ALA
12
A
PHE
13
n
13
PHE
13
A
TYR
14
n
14
TYR
14
A
GLU
15
n
15
GLU
15
A
ILE
16
n
16
ILE
16
A
LEU
17
n
17
LEU
17
A
HIS
18
n
18
HIS
18
A
LEU
19
n
19
LEU
19
A
PRO
20
n
20
PRO
20
A
ASN
21
n
21
ASN
21
A
LEU
22
n
22
LEU
22
A
ASN
23
n
23
ASN
23
A
GLU
24
n
24
GLU
24
A
GLU
25
n
25
GLU
25
A
GLN
26
n
26
GLN
26
A
ARG
27
n
27
ARG
27
A
ASN
28
n
28
ASN
28
A
ALA
29
n
29
ALA
29
A
PHE
30
n
30
PHE
30
A
ILE
31
n
31
ILE
31
A
GLN
32
n
32
GLN
32
A
SER
33
n
33
SER
33
A
LEU
34
n
34
LEU
34
A
LYS
35
n
35
LYS
35
A
ASP
36
n
36
ASP
36
A
ASP
37
n
37
ASP
37
A
PRO
38
n
38
PRO
38
A
SER
39
n
39
SER
39
A
GLN
40
n
40
GLN
40
A
SER
41
n
41
SER
41
A
ALA
42
n
42
ALA
42
A
ASN
43
n
43
ASN
43
A
LEU
44
n
44
LEU
44
A
LEU
45
n
45
LEU
45
A
ALA
46
n
46
ALA
46
A
GLU
47
n
47
GLU
47
A
ALA
48
n
48
ALA
48
A
LYS
49
n
49
LYS
49
A
LYS
50
n
50
LYS
50
A
LEU
51
n
51
LEU
51
A
ASN
52
n
52
ASN
52
A
ASP
53
n
53
ASP
53
A
ALA
54
n
54
ALA
54
A
GLN
55
n
55
GLN
55
A
ALA
56
n
56
ALA
56
A
PRO
57
n
57
PRO
57
A
LYS
58
n
58
LYS
58
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
4
A
A
O
OE1
LEU
GLN
51
55
1.93
1
A
LYS
4
-93.74
-82.33
1
A
GLN
40
-95.60
31.11
2
A
ASP
2
-56.34
-89.50
2
A
ASN
3
-160.09
-164.25
2
A
LYS
4
-87.03
-88.90
2
A
PRO
38
-55.10
-135.44
2
A
GLN
40
-84.23
31.62
2
A
PRO
57
-52.75
173.42
3
A
LYS
4
-100.04
45.19
3
A
PRO
38
-54.61
-134.68
3
A
GLN
40
-80.47
41.23
4
A
ASP
2
-67.74
-174.27
4
A
ASN
3
-69.94
-123.00
5
A
ASN
3
-94.54
48.44
5
A
LYS
4
-100.04
61.56
5
A
ALA
56
-53.48
106.62
6
A
ASP
2
-69.59
-172.42
6
A
PHE
5
-76.31
-164.43
7
A
LYS
4
-51.75
-84.66
7
A
PRO
38
-55.80
-136.97
8
A
PRO
38
-50.40
-155.87
8
A
GLN
40
-77.48
33.98
9
A
ASN
3
-108.31
-143.19
9
A
LYS
4
-100.04
-147.70
9
A
GLU
25
-54.13
-72.57
10
A
LYS
4
-65.52
-124.98
10
A
PHE
5
-69.91
-172.07
10
A
ASN
6
-149.85
-104.65
REFINED Solution NMR structure of the Z domain of STAPHYLOCOCCAL PROTEIN A
1
N
N
A
ASN
6
A
ASN
6
HELX_P
A
HIS
18
A
HIS
18
1
1
13
A
ASN
23
A
ASN
23
HELX_P
A
ASP
37
A
ASP
37
1
2
15
A
GLN
40
A
GLN
40
HELX_P
A
GLN
55
A
GLN
55
1
3
16
IMMUNE SYSTEM
IMMUNOGLOBULIN-BINDING PROTEIN, THREE-HELICAL BUNDLE STRUCTURE, RESIDUAL DIPOLAR COUPLINGS, IMMUNE SYSTEM
SPA2_STAAU
UNP
1
212
P38507
ADNKFNKEQQNAFYEILHLPNLNEEQRNGFIQSLKDDPSQSANLLAEAKKLNDAQAPK
212
269
1Q2N
1
58
P38507
A
1
1
58
1
ALA
engineered mutation
VAL
1
1Q2N
A
P38507
UNP
212
1
1
GLY
engineered mutation
ALA
29
1Q2N
A
P38507
UNP
240
29
1
P 1