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