0.037193
0.000000
0.000000
0.000000
0.037965
0.000000
0.000000
0.000000
0.049290
0.000000
0.000000
0.000000
Vitagliano, L.
Berisio, R.
Mazzarella, L.
Zagari, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
26.887
26.340
20.288
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
N
N
2
N
C
N
3
N
C
N
4
N
O
N
5
N
O
N
6
N
H
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
O
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
O
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
doub
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
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
US
Biopolymers
BIPMAA
0161
0006-3525
58
459
464
10.1002/1097-0282(20010415)58:5<459::AID-BIP1021>3.0.CO;2-V
11241217
Structural bases of collagen stabilization induced by proline hydroxylation.
2001
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
56
55
61
10.1107/S0907444999014158
Effects of microgravity on the crystal quality of a collagen-like polypeptide
2000
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
280
623
638
10.1006/jmbi.1998.1881
X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)
1998
10.2210/pdb1g9w/pdb
pdb_00001g9w
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
293
1
IMAGE PLATE
1998-12-01
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.004
1.0
5.2R
ELETTRA
1.004
SYNCHROTRON
ELETTRA BEAMLINE 5.2R
771.859
COLLAGEN-LIKE PEPTIDE
1
syn
polymer
520.578
COLLAGEN-LIKE PEPTIDE
2
syn
polymer
18.015
water
36
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
1.97
37.43
DIALYSIS
SODIUM ACETATE, ACETIC ACID, DIALYSIS, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Refinement description
1
0
2001-04-18
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
1
4
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2000-11-28
REL
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.
1A3J
PDB
experimental model
HOH
1001
3
HOH
HOH
1001
A
HOH
1002
3
HOH
HOH
1002
A
HOH
1003
3
HOH
HOH
1003
A
HOH
1004
3
HOH
HOH
1004
A
HOH
1005
3
HOH
HOH
1005
A
HOH
1006
3
HOH
HOH
1006
A
HOH
1007
3
HOH
HOH
1007
A
HOH
1008
3
HOH
HOH
1008
A
HOH
1009
3
HOH
HOH
1009
A
HOH
1022
3
HOH
HOH
1022
A
HOH
1023
3
HOH
HOH
1023
A
HOH
1024
3
HOH
HOH
1024
A
HOH
1025
3
HOH
HOH
1025
A
HOH
1026
3
HOH
HOH
1026
A
HOH
1028
3
HOH
HOH
1028
A
HOH
1030
3
HOH
HOH
1030
A
HOH
1034
3
HOH
HOH
1034
A
HOH
1036
3
HOH
HOH
1036
A
HOH
1037
3
HOH
HOH
1037
A
HOH
1010
3
HOH
HOH
1010
B
HOH
1011
3
HOH
HOH
1011
B
HOH
1012
3
HOH
HOH
1012
B
HOH
1013
3
HOH
HOH
1013
B
HOH
1014
3
HOH
HOH
1014
B
HOH
1021
3
HOH
HOH
1021
B
HOH
1029
3
HOH
HOH
1029
B
HOH
1035
3
HOH
HOH
1035
B
HOH
1015
3
HOH
HOH
1015
C
HOH
1016
3
HOH
HOH
1016
C
HOH
1017
3
HOH
HOH
1017
C
HOH
1018
3
HOH
HOH
1018
C
HOH
1019
3
HOH
HOH
1019
C
HOH
1020
3
HOH
HOH
1020
C
HOH
1027
3
HOH
HOH
1027
C
HOH
1031
3
HOH
HOH
1031
C
HOH
1032
3
HOH
HOH
1032
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
0.1460000
0.1470000
0.1900000
0.1940000
20
20
309
author_and_software_defined_assembly
PISA
3
trimeric
1020
-7
1540
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
A
B
N
C
PRO
GLY
1
36
1.30
1_555
1_556
1
B
C
N
C
PRO
GLY
31
66
1.34
1_555
1_556
1
A
C
C
N
GLY
PRO
9
61
1.34
1_555
1_554
DUE TO THE QUASI-INFINITE 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.
0.1940000
0.1470000
1.30
10.00
147
320
179
20
89.0
RANDOM
1
THROUGHOUT
0
PDB1A3J.ENT
ENGH AND HUBER
162.
1.30
10.00
36
162
0
0
126
0.015
0.026
1.3
15
1G9W
3448
0.0420000
1
4.8
89.0
0.0930000
1.3
1.33
66.4
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
STRUCTURAL BASIS OF COLLAGEN STABILIZATION INDUCED BY PROLINE HYDROXYLATION
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
THE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE
TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90
RESIDUE PEPTIDE.
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.
STRUCTURAL PROTEIN
COLLAGEN, EXTRACELLULAR MATRIX, STRUCTURAL PROTEIN
1G9W
PDB
1
1G9W
1G9W
PDB
2
1G9W
1
9
1G9W
1
9
1G9W
A
1
1
9
31
36
1G9W
31
36
1G9W
B
2
1
6
61
66
1G9W
61
66
1G9W
C
2
1
6
19
P 21 21 21