1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Sticht, H. Ejchart, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE 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 H13 N O2 131.173 y ISOLEUCINE L-peptide linking La 3 138.905 LANTHANUM (III) ION non-polymer C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking H2 N 16.023 AMINO GROUP non-polymer C3 H7 N O3 105.093 y SERINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 96 903 908 10.1073/pnas.96.3.903 9927666 Alpha-helix nucleation by a calcium-binding peptide loop. 1999 10.2210/pdb1nkf/pdb pdb_00001nkf 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 LA3+ ION BOUND 1606.649 CALCIUM-BINDING HEXADECAPEPTIDE D5N 1 man polymer 138.905 LANTHANUM (III) ION 1 syn non-polymer CALMODULIN no yes (ACE)DKDGDGYISAAEAAAQ(NH2) XDKDGDGYISAAEAAAQX A polypeptide(L) n n n n n n n n n n n n n n n n n n human Homo sample 9606 Homo sapiens database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1999-02-16 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_conn.pdbx_leaving_atom_flag _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.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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1998-03-09 REL REL LA LANTHANUM (III) ION ENERGY, AGREEMENT WITH EXPERIMENTAL DATA 100 30 NOESY TOCSY COSY 1H-13C-HMQC 120mM 6.0 10E+5 PA atm 275.2 K DESCRIPTION OF THE STRATEGY USED FOR NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES ACCORDING TO THEIR INTENSITY: STRONG, 0.18 - 0.27 NM; MEDIUM, 0.18 - 0.40 NM; WEAK, 0.18 - 0.55 NM. PEAK INTENSITIES WERE ESTIMATED FROM THE NUMBER OF CONTOURS IN NOESY SPECTRUM. HARMONIC RESTRAINTS FOR THE LA3+-ION WERE DEDUCED FROM THE POSITION OF THE CORRESPONDING CA2+-ION CRYSTAL STRUCTURE OF CALMODULIN (PDB CODE: 1CDM). A TOTAL OF SIX HARMONIC DISTANCE RESTRAINTS WAS INCLUDED IN ORDER TO FIX THE DISTANCE AND THE OCTAHEDRAL ARRANGEMENT OF THE SIX LIGANDS RELATIVE TO THE LA3+-ION ASSUMING THE SAME COORDINATION AS FOR THE CA2+ ION IN THE CALMODULIN CRYSTAL STRUCTURE. THE STRUCTURE CALCULATIONS USED THE AB INITIO SIMULATED ANNEALING (SA.INP) AND REFINEMENT (REFINE.INP) PROTOCOLS FROM THE X-PLOR PROGRAM PACKAGE. THE CALCULATIONS STARTED FROM AN EXTENDED TEMPLATE WITH RANDOMIZED BACKBONE TORSION ANGLES FOLLOWED BY 50 CYCLES OF ENERGY MINIMIZATION TO REMOVE CLOSE NON-BONDED CONTACTS. THE HIGH TEMPERATURE PHASE COMPRISED 50 PS OF DYNAMICS AT 1000 K; THE FINAL 16 PS HAD AN INCREASED WEIGHT ON COVALENT GEOMETRY RESTRAINTS AND THE NOE DERIVED DISTANCE RESTRAINTS. IN THE NEXT PHASE THE SYSTEM WAS SLOWLY COOLED FROM 1000 K TO 100 K IN A TIME OF 30 PS FOLLOWED BY 200 STEPS OF ENERGY MINIMIZATION. FOR THE NOE EFFECTIVE ENERGY TERM, REPRESENTING THE INTERPROTON DISTANCES, A SOFT SQUARE-WELL POTENTIAL WAS APPLIED. THE REFINEMENT PROTOCOL CONSISTED OF A SLOW-COOLING FROM 1000 TO 100 K WITHIN 45 PS. A FORCE CONSTANT OF 200 KCAL MOL-1 RAD-1 WAS USED FOR THE DIHEDRAL ANGLE RESTRAINTS WHILE THE NOE DERIVED DISTANCE RESTRAINTS AND HARMONIC RESTRAINT WERE REPRESENTED BY A SQUARE-WELL POTENTIAL FUNCTION WITH FORCE CONSTANT OF 50 KCAL/MOL1/A2. OF THE 200 RESULTING STRUCTURES, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST ENERGY AND THE LEAST VIOLATION OF THE EXPERIMENTAL DATA WERE SELECTED FOR FURTHER CHARACTERIZATION. GEOMETRY OF THE STRUCTURES AND ELEMENTS OF SECONDARY STRUCTURE WERE ANALYZED USING PROCHECK AND DSSP. SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS 1 H2O/D2O(9:1) BRUNGER refinement X-PLOR structure solution NDEE structure solution X-PLOR 600 Bruker AMX600 LA 18 2 LA LA 18 A ACE 0 n 1 ACE 0 A ASP 1 n 2 ASP 1 A LYS 2 n 3 LYS 2 A ASP 3 n 4 ASP 3 A GLY 4 n 5 GLY 4 A ASP 5 n 6 ASP 5 A GLY 6 n 7 GLY 6 A TYR 7 n 8 TYR 7 A ILE 8 n 9 ILE 8 A SER 9 n 10 SER 9 A ALA 10 n 11 ALA 10 A ALA 11 n 12 ALA 11 A GLU 12 n 13 GLU 12 A ALA 13 n 14 ALA 13 A ALA 14 n 15 ALA 14 A ALA 15 n 16 ALA 15 A GLN 16 n 17 GLN 16 A NH2 17 n 18 NH2 17 A author_defined_assembly 1 monomeric A ASP 5 A OD1 ASP 6 1_555 A LA 18 B LA LA 1_555 A GLU 12 A OE2 GLU 13 1_555 152.3 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 A O H GLU ALA 12 15 1.60 3 A A OD2 H ASP GLY 1 6 1.48 4 A A OD2 H ASP GLY 1 6 1.59 6 A A O H SER ALA 9 13 1.59 11 A A O H SER ALA 9 13 1.59 13 A A O HN2 ALA NH2 13 17 1.49 13 A A O HE21 GLU GLN 12 16 1.58 14 A A O H SER ALA 9 13 1.56 14 A A H OE1 SER GLU 9 12 1.59 16 A A O H SER ALA 9 13 1.58 16 A A H OE1 SER GLU 9 12 1.59 17 A A H OE1 SER GLU 9 12 1.59 19 A A O H SER ALA 9 13 1.52 20 A A H OE1 SER GLU 9 12 1.57 21 A A H OE1 SER GLU 9 12 1.55 22 A A H OE1 SER GLU 9 12 1.56 22 A A O H SER ALA 9 13 1.57 23 A A H OE1 SER GLU 9 12 1.54 23 A A O H SER ALA 9 13 1.55 24 A A O H SER ALA 9 13 1.56 25 A A H OE1 SER GLU 9 12 1.55 25 A A O H SER ALA 9 13 1.57 28 A A O H SER ALA 9 13 1.54 29 A A O H SER ALA 9 13 1.54 29 A A H OE1 SER GLU 9 12 1.57 30 A A OD2 H ASP GLY 1 6 1.45 30 A A OD2 H ASP ASP 1 5 1.55 1 A ALA 10 -54.97 -75.94 3 A ALA 10 -61.49 -73.01 5 A ALA 10 -62.80 -71.80 7 A ALA 10 -65.02 -73.89 8 A ALA 10 -63.87 -70.76 10 A ALA 10 -65.42 -73.34 11 A ALA 10 -60.72 -74.50 12 A ASP 3 -137.50 -44.53 13 A ALA 10 -58.91 -72.63 14 A ALA 10 -59.34 -76.06 16 A ALA 10 -55.53 -72.81 17 A ALA 10 -60.93 -71.48 20 A ALA 10 -63.61 -74.54 22 A ALA 10 -52.01 -73.94 23 A ALA 10 -57.59 -74.80 24 A ALA 10 -45.26 -71.98 26 A ALA 10 -62.91 -75.65 27 A ALA 10 -63.79 -72.24 28 A ASP 3 -104.39 -63.64 28 A ALA 10 -44.98 -70.92 model building X-PLOR refinement X-PLOR phasing X-PLOR CALCIUM-BINDING PEPTIDE, NMR, 30 STRUCTURES 1 Y N 2 N N A ALA 10 A ALA 11 HELX_P A ALA 14 A ALA 15 1 1 5 covale 1.305 both A ACE 0 A C ACE 1 1_555 A ASP 1 A N ASP 2 1_555 covale 1.305 both A GLN 16 A C GLN 17 1_555 A NH2 17 A N NH2 18 1_555 metalc 2.379 A ASP 5 A OD1 ASP 6 1_555 A LA 18 B LA LA 1_555 metalc 2.383 A GLU 12 A OE2 GLU 13 1_555 A LA 18 B LA LA 1_555 CALCIUM-BINDING EF HAND CALCIUM BINDING LOOP, ALPHA-HELIX, CALCIUM-BINDING CALM_HUMAN UNP 1 1 P02593 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 93 104 1NKF 1 12 P02593 A 1 2 13 1 ASN conflict ASP 5 1NKF A P02593 UNP 97 6 BINDING SITE FOR RESIDUE LA A 18 A LA 18 Software 5 A ASP 1 A ASP 2 5 1_555 A ASP 3 A ASP 4 5 1_555 A ASP 5 A ASP 6 5 1_555 A TYR 7 A TYR 8 5 1_555 A GLU 12 A GLU 13 5 1_555 1 P 1