0.037286
0.000000
0.000000
0.000000
0.038037
0.000000
0.000000
0.000000
0.049554
0.00000
0.00000
0.00000
Kramer, R.Z.
Vitagliano, L.
Bella, J.
Berisio, R.
Mazzarella, L.
Brodsky, B.
Zagari, A.
Berman, H.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
26.820
26.290
20.180
C2 H4 O2
60.052
ACETIC ACID
non-polymer
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
H2 O
18.015
WATER
non-polymer
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
N
1
N
C
N
2
N
O
N
3
N
O
N
4
N
C
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
H
N
9
N
N
N
10
N
C
N
11
N
C
N
12
N
O
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
O
N
20
N
H
N
21
N
H
N
22
N
N
N
23
S
C
N
24
N
C
N
25
N
O
N
26
N
C
N
27
N
C
N
28
N
C
N
29
N
O
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
doub
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
doub
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
280
623
638
10.1006/jmbi.1998.1881
9677293
X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly).
1998
10.2210/pdb1a3i/pdb
pdb_00001a3i
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
0.00000
0.00000
20.18000
259.0
1
DIFFRACTOMETER
1991-10
ENRAF-NONIUS FAST
M
x-ray
1
1.5418
1.0
1.5418
771.859
COLLAGEN-LIKE PEPTIDE
1
man
polymer
520.578
COLLAGEN-LIKE PEPTIDE
2
man
polymer
60.052
ACETIC ACID
2
syn
non-polymer
18.015
water
37
nat
water
no
no
PPGPPGPPG
PPGPPGPPG
A
polypeptide(L)
no
no
PPGPPG
PPGPPG
B,C
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
1.95
36.82
PEPTIDE WAS CRYSTALLIZED FROM 4.0 MG/ML PEPTIDE IN 10% ACETIC ACID, 0.1% SODIUM AZIDE, AND 3.0% PEG400.
diffrn_detector
pdbx_database_status
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Other
Data collection
Database references
Derived calculations
Refinement description
1
0
1998-05-06
1
1
2008-03-24
1
2
2011-07-13
1
3
2018-04-18
1
4
2024-04-03
_diffrn_detector.detector
_pdbx_database_status.process_site
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-01-22
REL
REL
ACY
ACETIC ACID
HOH
water
HYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND
CRICK MODEL II FOR COLLAGEN.
FOR EACH CHAIN, RESIDUE NUMBERING CORRESPONDS TO THE ENTIRE
MOLECULE RATHER THAN THE SHORTER ASYMMETRIC UNIT.
IDEALIZED SEVEN-FOLD TRIPLE-HELIX
Other
in silico model
ACY
401
3
ACY
ACY
401
A
ACY
402
3
ACY
ACY
402
C
HOH
101
4
HOH
HOH
101
A
HOH
102
4
HOH
HOH
102
A
HOH
103
4
HOH
HOH
103
A
HOH
104
4
HOH
HOH
104
A
HOH
105
4
HOH
HOH
105
A
HOH
106
4
HOH
HOH
106
A
HOH
107
4
HOH
HOH
107
A
HOH
108
4
HOH
HOH
108
A
HOH
109
4
HOH
HOH
109
A
HOH
201
4
HOH
HOH
201
A
HOH
204
4
HOH
HOH
204
A
HOH
209
4
HOH
HOH
209
A
HOH
218
4
HOH
HOH
218
A
HOH
220
4
HOH
HOH
220
A
HOH
241
4
HOH
HOH
241
A
HOH
244
4
HOH
HOH
244
A
HOH
245
4
HOH
HOH
245
A
HOH
111
4
HOH
HOH
111
B
HOH
112
4
HOH
HOH
112
B
HOH
113
4
HOH
HOH
113
B
HOH
115
4
HOH
HOH
115
B
HOH
116
4
HOH
HOH
116
B
HOH
242
4
HOH
HOH
242
B
HOH
246
4
HOH
HOH
246
B
HOH
247
4
HOH
HOH
247
B
HOH
121
4
HOH
HOH
121
C
HOH
122
4
HOH
HOH
122
C
HOH
123
4
HOH
HOH
123
C
HOH
124
4
HOH
HOH
124
C
HOH
125
4
HOH
HOH
125
C
HOH
126
4
HOH
HOH
126
C
HOH
202
4
HOH
HOH
202
C
HOH
205
4
HOH
HOH
205
C
HOH
208
4
HOH
HOH
208
C
HOH
210
4
HOH
HOH
210
C
HOH
243
4
HOH
HOH
243
C
HOH
248
4
HOH
HOH
248
C
PRO
1
n
1
PRO
1
A
PRO
2
n
2
PRO
2
A
GLY
3
n
3
GLY
3
A
PRO
4
n
4
PRO
4
A
PRO
5
n
5
PRO
5
A
GLY
6
n
6
GLY
6
A
PRO
7
n
7
PRO
7
A
PRO
8
n
8
PRO
8
A
GLY
9
n
9
GLY
9
A
PRO
31
n
1
PRO
31
B
PRO
32
n
2
PRO
32
B
GLY
33
n
3
GLY
33
B
PRO
34
n
4
PRO
34
B
PRO
35
n
5
PRO
35
B
GLY
36
n
6
GLY
36
B
PRO
61
n
1
PRO
61
C
PRO
62
n
2
PRO
62
C
GLY
63
n
3
GLY
63
C
PRO
64
n
4
PRO
64
C
PRO
65
n
5
PRO
65
C
GLY
66
n
6
GLY
66
C
author_defined_assembly
15
pentadecameric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_556
x,y,z+1
crystal symmetry operation
0.0000000000
0.0000000000
20.1800000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_557
x,y,z+2
crystal symmetry operation
0.0000000000
0.0000000000
40.3600000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_558
x,y,z+3
crystal symmetry operation
0.0000000000
0.0000000000
60.5400000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_559
x,y,z+4
crystal symmetry operation
0.0000000000
0.0000000000
80.7200000000
1
A
PRO
2
-56.35
171.52
1
A
PRO
5
-47.11
164.30
PARHCSDX.PRO
TOPHCSDX.PRO
15.9
DUE TO THE QUASI-INFINITE, AVERAGED NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL AXIS AND TIGHT REFINEMENT CONSTRAINTS WERE MAINTAINED.
THE UNIT CELL AXES WERE CHOSEN TO COINCIDE WITH A
PREVIOUS STRUCTURE DETERMINATION (OKUYAMA 1981) OF THIS
PEPTIDE.
0.1810000
0.1810000
1.97
8.
861
76.7
1000000.
0.1
1
GROUP
2.
MOLECULAR REPLACEMENT
IDEALIZED SEVEN-FOLD TRIPLE-HELIX
1.97
8.
45
171
0
0
126
0.01
2.07
2.11
0.2200000
2.04
69
10
63.3
1.97
1A3I
1136
0.
1
99.5
1.97
2.2
98.
model building
X-PLOR
3.1
refinement
LALS
data reduction
MOLEN
phasing
X-PLOR
3.1
refinement
X-PLOR
X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
THE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE
TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90
RESIDUE PEPTIDE DUE TO TRANSLATIONAL DISORDER ALONG THE
HELICAL AXIS. THE RESULT IS A POLYMER-LIKE STRUCTURE WITH
NO DEFINED ENDS.
THE POLYMER STRUCTURE IS FORMED BY CONTINUATION OF THE
CHAINS USING THE SYMMETRY-RELATED MOLECULES ALONG THE
HELICAL AXIS. THE TVECT RECORD BELOW PRESENTS THE
TRANSLATION THAT WILL GENERATE THE POLYMER. NOTE:
THEREFORE, CLOSE CONTACTS BETWEEN SYMMETRY-RELATED
MOLECULES ARE INTENTIONAL AND NECESSARY. INTERCHAIN
HYDROGEN BONDING AT THE END OF CHAINS ALSO UTILIZES
SYMMETRY-RELATED MOLECULES.
THE ENTIRE 30 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM
THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING
TRANSLATIONS (USING FRACTIONAL COORDINATES):
CHAIN A: TRANSLATE RESIDUES 1 - 9 BY (0 0 1), (0 0 2), AND
(0 0 3) AND RESIDUES 7 - 9 BY (0 0 4).
CHAIN B: TRANSLATE RESIDUES 31 - 36 BY (0 0 1), (0 0 2),
AND (0 0 3).
CHAIN C: TRANSLATE RESIDUES 61 - 66 BY (0 0 1), (0 0 2),
AND (0 0 3) AND RESIDUES 64 - 66 BY (004).
THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES,
30 IN EACH CHAIN.
covale
1.340
both
A
PRO
1
A
N
PRO
1
1_555
B
GLY
36
B
C
GLY
6
1_556
covale
1.309
both
A
GLY
9
A
C
GLY
9
1_556
C
PRO
61
C
N
PRO
1
1_555
covale
1.328
both
B
PRO
31
B
N
PRO
1
1_555
C
GLY
66
C
C
GLY
6
1_556
EXTRACELLULAR MATRIX
COLLAGEN, EXTRACELLULAR MATRIX
1A3I
PDB
1
1A3I
1A3I
PDB
2
1A3I
1
9
1A3I
1
9
1A3I
A
1
1
9
31
36
1A3I
31
36
1A3I
B
2
1
6
61
66
1A3I
61
66
1A3I
C
2
1
6
BINDING SITE FOR RESIDUE ACY A 401
A
ACY
401
Software
7
BINDING SITE FOR RESIDUE ACY C 402
C
ACY
402
Software
5
A
PRO
5
A
PRO
5
7
1_555
A
PRO
8
A
PRO
8
7
2_575
A
HOH
103
F
HOH
7
1_555
A
HOH
218
F
HOH
7
1_555
C
PRO
64
C
PRO
4
7
4_466
C
HOH
122
H
HOH
7
4_466
C
ACY
402
E
ACY
7
4_466
A
ACY
401
D
ACY
5
4_566
B
PRO
34
B
PRO
4
5
4_566
B
HOH
247
G
HOH
5
4_566
C
HOH
122
H
HOH
5
1_555
C
HOH
202
H
HOH
5
1_555
19
P 21 21 21