HEADER CALCIUM-BINDING 09-MAR-98 1NKF
TITLE CALCIUM-BINDING PEPTIDE, NMR, 30 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CALCIUM-BINDING HEXADECAPEPTIDE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CALMODULIN;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 OTHER_DETAILS: LA3+ ION BOUND
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS EF HAND CALCIUM BINDING LOOP, ALPHA-HELIX, CALCIUM-BINDING
EXPDTA SOLUTION NMR
NUMMDL 30
AUTHOR H.STICHT,A.EJCHART
REVDAT 4 23-FEB-22 1NKF 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 1NKF 1 VERSN
REVDAT 2 23-MAR-99 1NKF 1 COMPND REMARK TITLE HEADER
REVDAT 2 2 1 SOURCE JRNL KEYWDS
REVDAT 1 16-FEB-99 1NKF 0
JRNL AUTH M.SIEDLECKA,G.GOCH,A.EJCHART,H.STICHT,A.BIERZYSKI
JRNL TITL ALPHA-HELIX NUCLEATION BY A CALCIUM-BINDING PEPTIDE LOOP.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 903 1999
JRNL REFN ISSN 0027-8424
JRNL PMID 9927666
JRNL DOI 10.1073/PNAS.96.3.903
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: DESCRIPTION OF THE STRATEGY USED FOR
REMARK 3 NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE
REMARK 3 DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES
REMARK 3 ACCORDING TO THEIR INTENSITY: STRONG, 0.18 - 0.27 NM; MEDIUM,
REMARK 3 0.18 - 0.40 NM; WEAK, 0.18 - 0.55 NM. PEAK INTENSITIES WERE
REMARK 3 ESTIMATED FROM THE NUMBER OF CONTOURS IN NOESY SPECTRUM.
REMARK 3 HARMONIC RESTRAINTS FOR THE LA3+-ION WERE DEDUCED FROM THE
REMARK 3 POSITION OF THE CORRESPONDING CA2+-ION CRYSTAL STRUCTURE OF
REMARK 3 CALMODULIN (PDB CODE: 1CDM). A TOTAL OF SIX HARMONIC DISTANCE
REMARK 3 RESTRAINTS WAS INCLUDED IN ORDER TO FIX THE DISTANCE AND THE
REMARK 3 OCTAHEDRAL ARRANGEMENT OF THE SIX LIGANDS RELATIVE TO THE LA3+-
REMARK 3 ION ASSUMING THE SAME COORDINATION AS FOR THE CA2+ ION IN THE
REMARK 3 CALMODULIN CRYSTAL STRUCTURE. THE STRUCTURE CALCULATIONS USED
REMARK 3 THE AB INITIO SIMULATED ANNEALING (SA.INP) AND REFINEMENT
REMARK 3 (REFINE.INP) PROTOCOLS FROM THE X-PLOR PROGRAM PACKAGE. THE
REMARK 3 CALCULATIONS STARTED FROM AN EXTENDED TEMPLATE WITH RANDOMIZED
REMARK 3 BACKBONE TORSION ANGLES FOLLOWED BY 50 CYCLES OF ENERGY
REMARK 3 MINIMIZATION TO REMOVE CLOSE NON-BONDED CONTACTS. THE HIGH
REMARK 3 TEMPERATURE PHASE COMPRISED 50 PS OF DYNAMICS AT 1000 K; THE
REMARK 3 FINAL 16 PS HAD AN INCREASED WEIGHT ON COVALENT GEOMETRY
REMARK 3 RESTRAINTS AND THE NOE DERIVED DISTANCE RESTRAINTS. IN THE NEXT
REMARK 3 PHASE THE SYSTEM WAS SLOWLY COOLED FROM 1000 K TO 100 K IN A
REMARK 3 TIME OF 30 PS FOLLOWED BY 200 STEPS OF ENERGY MINIMIZATION. FOR
REMARK 3 THE NOE EFFECTIVE ENERGY TERM, REPRESENTING THE INTERPROTON
REMARK 3 DISTANCES, A SOFT SQUARE-WELL POTENTIAL WAS APPLIED. THE
REMARK 3 REFINEMENT PROTOCOL CONSISTED OF A SLOW-COOLING FROM 1000 TO 100
REMARK 3 K WITHIN 45 PS. A FORCE CONSTANT OF 200 KCAL MOL-1 RAD-1 WAS
REMARK 3 USED FOR THE DIHEDRAL ANGLE RESTRAINTS WHILE THE NOE DERIVED
REMARK 3 DISTANCE RESTRAINTS AND HARMONIC RESTRAINT WERE REPRESENTED BY A
REMARK 3 SQUARE-WELL POTENTIAL FUNCTION WITH FORCE CONSTANT OF 50 KCAL/
REMARK 3 MOL1/A2. OF THE 200 RESULTING STRUCTURES, THOSE 30 STRUCTURES
REMARK 3 THAT SHOWED THE LOWEST ENERGY AND THE LEAST VIOLATION OF THE
REMARK 3 EXPERIMENTAL DATA WERE SELECTED FOR FURTHER CHARACTERIZATION.
REMARK 3 GEOMETRY OF THE STRUCTURES AND ELEMENTS OF SECONDARY STRUCTURE
REMARK 3 WERE ANALYZED USING PROCHECK AND DSSP.
REMARK 4
REMARK 4 1NKF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000175319.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 275.2
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : 120MM
REMARK 210 PRESSURE : 10E+5 PA ATM
REMARK 210 SAMPLE CONTENTS : H2O/D2O(9:1)
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; COSY; 1H-13C-HMQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX600
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NDEE, X-PLOR
REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED
REMARK 210 MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30
REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY, AGREEMENT WITH
REMARK 210 EXPERIMENTAL DATA
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O GLU A 12 H ALA A 15 1.60
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ALA A 10 -75.94 -54.97
REMARK 500 3 ALA A 10 -73.01 -61.49
REMARK 500 5 ALA A 10 -71.80 -62.80
REMARK 500 7 ALA A 10 -73.89 -65.02
REMARK 500 8 ALA A 10 -70.76 -63.87
REMARK 500 10 ALA A 10 -73.34 -65.42
REMARK 500 11 ALA A 10 -74.50 -60.72
REMARK 500 12 ASP A 3 -44.53 -137.50
REMARK 500 13 ALA A 10 -72.63 -58.91
REMARK 500 14 ALA A 10 -76.06 -59.34
REMARK 500 16 ALA A 10 -72.81 -55.53
REMARK 500 17 ALA A 10 -71.48 -60.93
REMARK 500 20 ALA A 10 -74.54 -63.61
REMARK 500 22 ALA A 10 -73.94 -52.01
REMARK 500 23 ALA A 10 -74.80 -57.59
REMARK 500 24 ALA A 10 -71.98 -45.26
REMARK 500 26 ALA A 10 -75.65 -62.91
REMARK 500 27 ALA A 10 -72.24 -63.79
REMARK 500 28 ASP A 3 -63.64 -104.39
REMARK 500 28 ALA A 10 -70.92 -44.98
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 LA A 18 LA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 5 OD1
REMARK 620 2 GLU A 12 OE2 152.3
REMARK 620 N 1
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LA A 18
DBREF 1NKF A 1 12 UNP P02593 CALM_HUMAN 93 104
SEQADV 1NKF ASP A 5 UNP P02593 ASN 97 CONFLICT
SEQRES 1 A 18 ACE ASP LYS ASP GLY ASP GLY TYR ILE SER ALA ALA GLU
SEQRES 2 A 18 ALA ALA ALA GLN NH2
HET ACE A 0 6
HET NH2 A 17 3
HET LA A 18 1
HETNAM ACE ACETYL GROUP
HETNAM NH2 AMINO GROUP
HETNAM LA LANTHANUM (III) ION
FORMUL 1 ACE C2 H4 O
FORMUL 1 NH2 H2 N
FORMUL 2 LA LA 3+
HELIX 1 1 ALA A 10 ALA A 14 1 5
LINK C ACE A 0 N ASP A 1 1555 1555 1.31
LINK C GLN A 16 N NH2 A 17 1555 1555 1.31
LINK OD1 ASP A 5 LA LA A 18 1555 1555 2.38
LINK OE2 GLU A 12 LA LA A 18 1555 1555 2.38
SITE 1 AC1 5 ASP A 1 ASP A 3 ASP A 5 TYR A 7
SITE 2 AC1 5 GLU A 12
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
HETATM 1 C ACE A 0 25.255 61.378 61.870 1.00 0.00 C
HETATM 2 O ACE A 0 24.101 61.031 61.716 1.00 0.00 O
HETATM 3 CH3 ACE A 0 26.208 60.593 62.775 1.00 0.00 C
HETATM 4 H1 ACE A 0 25.697 59.728 63.171 1.00 0.00 H
HETATM 5 H2 ACE A 0 26.533 61.224 63.589 1.00 0.00 H
HETATM 6 H3 ACE A 0 27.066 60.274 62.202 1.00 0.00 H
(ATOM LINES ARE NOT SHOWN.)
END
