10 20 30 40 50 60 70 80 1NVO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER UNKNOWN FUNCTION 04-FEB-03 1NVO
TITLE SOLUTION STRUCTURE OF A FOUR-HELIX BUNDLE MODEL, APO-DF1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMODIMERIC ALPHA2 FOUR-HELIX BUNDLE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DE NOVO PROTEIN DESIGN, ALPHA-HELICAL BUNDLE, DIIRON KEYWDS 2 PROTEIN MODEL, UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 14
AUTHOR O.MAGLIO,F.NASTRI,V.PAVONE,A.LOMBARDI,W.F.DEGRADO
REVDAT 4 24-FEB-09 1NVO 1 VERSN REVDAT 3 13-JAN-04 1NVO 1 JRNL REVDAT 2 02-APR-03 1NVO 1 JRNL REVDAT 1 25-MAR-03 1NVO 0
JRNL AUTH O.MAGLIO,F.NASTRI,V.PAVONE,A.LOMBARDI,W.F.DEGRADO JRNL TITL PREORGANIZATION OF MOLECULAR BINDING SITES IN JRNL TITL 2 DESIGNED DIIRON PROTEINS JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 3772 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12655072 JRNL DOI 10.1073/PNAS.0730771100
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.LOMBARDI,C.M.SUMMA,S.GEREMIA,L.RANDACCIO, REMARK 1 AUTH 2 V.PAVONE,W.F.DEGRADO REMARK 1 TITL RETROSTRUCTURAL ANALYSIS OF METALLOPROTEINS. REMARK 1 TITL 2 APPLICATION TO THE DESIGN OF A MINIMAL MODEL FOR REMARK 1 TITL 3 DIIRON PROTEINS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 97 6298 2000 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.97.12.6298 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.M.SUMMA,A.LOMBARDI,M.LEWIS,W.F.DEGRADO REMARK 1 TITL TERTIARY TEMPLATES FOR THE DESIGN OF DIIRON PROTEIN REMARK 1 REF CURR.OPIN.STRUCT.BIOL. V. 9 500 1999 REMARK 1 REFN ISSN 0959-440X REMARK 1 DOI 10.1016/S0959-440X(99)80071-2 REMARK 1 REFERENCE 3 REMARK 1 AUTH L.DI COSTANZO,H.WADE,S.GEREMIA,L.RANDACCIO, REMARK 1 AUTH 2 V.PAVONE,W.F.DEGRADO,A.LOMBARDI REMARK 1 TITL TOWARD THE DE NOVO DESIGN OF A CATALYTICALLY REMARK 1 TITL 2 ACTIVE HELIX BUNDLE: A SUBSTRATE-ACCESSIBLE REMARK 1 TITL 3 CARBOXYLATE-BRIDGED DINUCLEAR METAL CENTER REMARK 1 REF J.AM.CHEM.SOC. V. 123 12749 2001 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA010506X REMARK 1 REFERENCE 4 REMARK 1 AUTH W.F.DEGRADO,L.DI COSTANZO,S.GEREMIA,A.LOMBARDI, REMARK 1 AUTH 2 V.PAVONE,L.RANDACCIO REMARK 1 TITL SLIDING HELIX AND CHANGE OF COORDINATION GEOMETRY REMARK 1 TITL 2 IN A MODEL DI-MN(II) PROTEIN REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 42 417 2003 REMARK 1 REFN ISSN 0570-0833 REMARK 1 DOI 10.1002/ANIE.200390127
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1NVO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-03. REMARK 100 THE RCSB ID CODE IS RCSB018255.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM PROTEIN CONCENTRATION; REMARK 210 90% H2O, 10% DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY, 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, ENERGY REMARK 210 RESTRAINED MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND REMARK 210 ENERGY,STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES
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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 TYR A 2 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 6 TYR A 2 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 TYR A 2 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES 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 LEU A 7 -43.46 -131.33 REMARK 500 1 GLU A 44 27.56 -75.92 REMARK 500 1 THR A 45 -51.01 -148.30 REMARK 500 1 LEU A 47 -54.14 72.53 REMARK 500 1 LEU B 7 -61.79 -145.59 REMARK 500 2 TYR A 2 -55.35 -19.10 REMARK 500 2 LEU A 6 37.51 -95.19 REMARK 500 2 LEU A 7 -57.83 -144.51 REMARK 500 2 ILE A 46 -58.31 -26.25 REMARK 500 2 LEU A 47 134.02 -170.71 REMARK 500 2 TYR B 2 -69.76 -26.81 REMARK 500 2 LEU B 7 -66.45 -151.39 REMARK 500 2 GLU B 44 35.75 -76.86 REMARK 500 2 THR B 45 -48.27 -150.22 REMARK 500 2 ILE B 46 66.22 36.21 REMARK 500 3 LEU A 7 -51.95 -130.99 REMARK 500 3 ILE A 46 67.55 35.67 REMARK 500 3 LEU A 47 16.20 57.87 REMARK 500 3 GLU B 5 -50.24 -137.44 REMARK 500 4 GLU A 5 -63.33 -102.59 REMARK 500 4 LEU A 6 33.97 -83.67 REMARK 500 4 LEU A 7 -55.47 -143.66 REMARK 500 4 GLU B 5 -74.07 -102.28 REMARK 500 4 LEU B 47 -138.47 64.63 REMARK 500 5 LEU A 7 -47.78 -135.67 REMARK 500 5 LYS A 25 63.99 61.69 REMARK 500 5 THR A 45 -46.43 -152.71 REMARK 500 5 LEU A 47 79.80 62.87 REMARK 500 5 LEU B 7 -62.66 -133.60 REMARK 500 5 GLU B 44 27.30 -75.47 REMARK 500 5 THR B 45 -45.46 -150.16 REMARK 500 5 ILE B 46 49.20 39.80 REMARK 500 6 LEU A 7 -58.09 -160.58 REMARK 500 6 GLU B 5 -69.46 -127.28 REMARK 500 6 LEU B 7 -53.77 -140.20 REMARK 500 6 LYS B 25 71.11 62.40 REMARK 500 6 ILE B 46 111.03 -27.28 REMARK 500 7 TYR A 2 -57.58 -20.01 REMARK 500 7 GLU A 5 -66.13 -98.23 REMARK 500 7 GLU B 5 -160.77 -112.65 REMARK 500 7 LEU B 7 -59.59 -177.62 REMARK 500 7 GLU B 44 36.94 -77.79 REMARK 500 7 THR B 45 -49.11 -156.65 REMARK 500 7 ILE B 46 -136.55 43.69 REMARK 500 8 LEU A 3 66.61 -164.12 REMARK 500 8 ARG A 4 -7.65 -153.89 REMARK 500 8 LEU A 7 -51.95 -129.18 REMARK 500 8 GLU B 5 -76.88 -125.73 REMARK 500 8 LEU B 6 6.78 -68.02 REMARK 500 8 LEU B 7 -56.31 -127.49 REMARK 500 8 THR B 45 -46.28 -143.96 REMARK 500 9 LEU A 7 -52.93 -160.76 REMARK 500 9 PRO A 27 39.29 -76.06 REMARK 500 9 GLU A 44 30.51 -76.58 REMARK 500 9 THR A 45 -44.23 -154.59 REMARK 500 9 GLU B 5 -69.39 -120.55 REMARK 500 9 LEU B 7 -53.65 -122.95 REMARK 500 9 LEU B 21 -65.06 -96.62 REMARK 500 9 VAL B 24 -92.56 -88.69 REMARK 500 9 LYS B 25 26.85 173.38 REMARK 500 9 GLU B 44 35.36 -81.93 REMARK 500 9 THR B 45 -47.08 -148.21 REMARK 500 9 ILE B 46 63.13 37.88 REMARK 500 10 TYR A 2 -53.38 -10.46 REMARK 500 10 LEU A 7 -50.92 -136.00 REMARK 500 10 GLU A 44 38.93 -76.99 REMARK 500 10 THR A 45 -28.04 -162.86 REMARK 500 10 ILE A 46 98.15 -55.55 REMARK 500 10 LEU A 47 164.27 65.68 REMARK 500 10 LEU B 7 -65.73 -104.02 REMARK 500 10 GLU B 44 28.62 -75.43 REMARK 500 10 THR B 45 -49.82 -151.08 REMARK 500 11 TYR A 2 -49.38 -22.36 REMARK 500 11 LEU A 3 -30.40 -130.39 REMARK 500 11 LEU A 7 -70.36 -153.04 REMARK 500 11 TYR B 2 -67.00 -26.90 REMARK 500 11 LEU B 7 -62.20 -148.43 REMARK 500 11 GLU B 44 26.60 -71.26 REMARK 500 11 THR B 45 -45.09 -154.06 REMARK 500 12 LEU A 3 40.42 -88.95 REMARK 500 12 LEU A 6 2.83 -69.51 REMARK 500 12 GLU A 44 22.02 -75.80 REMARK 500 12 THR A 45 -54.15 -146.17 REMARK 500 12 ILE A 46 157.65 57.20 REMARK 500 12 GLU B 5 -71.11 -89.81 REMARK 500 12 GLU B 44 29.29 -78.42 REMARK 500 12 THR B 45 -42.29 -153.37 REMARK 500 13 ILE A 46 101.64 -43.59 REMARK 500 13 LEU A 47 -53.70 -166.13 REMARK 500 13 LEU B 7 -63.15 -135.45 REMARK 500 13 LYS B 25 71.13 56.98 REMARK 500 14 LEU A 7 -58.04 -152.27 REMARK 500 14 LEU A 47 -70.08 66.37 REMARK 500 14 LEU B 6 38.30 -84.92 REMARK 500 14 LEU B 7 -72.19 -153.92 REMARK 500 14 GLU B 44 25.75 -74.07 REMARK 500 14 THR B 45 -45.69 -147.90 REMARK 500 14 LEU B 47 86.04 -69.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 2 0.09 SIDE_CHAIN REMARK 500 1 TYR B 2 0.07 SIDE_CHAIN REMARK 500 1 TYR B 17 0.09 SIDE_CHAIN REMARK 500 2 TYR B 2 0.10 SIDE_CHAIN REMARK 500 3 TYR A 2 0.18 SIDE_CHAIN REMARK 500 3 TYR A 17 0.09 SIDE_CHAIN REMARK 500 3 TYR B 2 0.07 SIDE_CHAIN REMARK 500 4 TYR A 2 0.08 SIDE_CHAIN REMARK 500 4 TYR B 2 0.07 SIDE_CHAIN REMARK 500 4 TYR B 17 0.09 SIDE_CHAIN REMARK 500 5 TYR A 17 0.07 SIDE_CHAIN REMARK 500 6 TYR B 2 0.08 SIDE_CHAIN REMARK 500 7 TYR A 17 0.13 SIDE_CHAIN REMARK 500 8 TYR B 2 0.09 SIDE_CHAIN REMARK 500 9 TYR B 2 0.09 SIDE_CHAIN REMARK 500 10 TYR A 2 0.07 SIDE_CHAIN REMARK 500 10 TYR A 23 0.08 SIDE_CHAIN REMARK 500 11 TYR A 17 0.09 SIDE_CHAIN REMARK 500 12 TYR A 17 0.14 SIDE_CHAIN REMARK 500 12 TYR B 2 0.14 SIDE_CHAIN REMARK 500 13 TYR A 2 0.10 SIDE_CHAIN REMARK 500 13 TYR A 17 0.07 SIDE_CHAIN REMARK 500 13 ARG B 4 0.09 SIDE_CHAIN REMARK 500 13 TYR B 17 0.07 SIDE_CHAIN REMARK 500 14 TYR B 17 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 49 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 49
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EC5 RELATED DB: PDB REMARK 900 1EC5 IS THE CRYSTAL STRUCTURE OF DF1-DI-ZN(II) DERIVATIVE REMARK 900 RELATED ID: 1JMB RELATED DB: PDB REMARK 900 1JMB IS THE CRYSTAL STRUCTURE OF A DF1 MUTANT (L13A-DF1) IN REMARK 900 THE DI-MN(II) FORM (S.G. C 2 2 21) REMARK 900 RELATED ID: 1JM0 RELATED DB: PDB REMARK 900 1JM0 IS A DIFFERENT CRYSTALLINE FORM (S. G. P212121) OF 1JMB REMARK 900 RELATED ID: 1LT1 RELATED DB: PDB REMARK 900 1LT1 IS THE CRYSTAL STRUCTURE OF L13G-DF1 IN THE DI-MN(II) REMARK 900 FORM
DBREF 1NVO A 0 49 PDB 1NVO 1NVO 0 49 DBREF 1NVO B 0 49 PDB 1NVO 1NVO 0 49
SEQRES 1 A 50 ACE ASP TYR LEU ARG GLU LEU LEU LYS LEU GLU LEU GLN SEQRES 2 A 50 LEU ILE LYS GLN TYR ARG GLU ALA LEU GLU TYR VAL LYS SEQRES 3 A 50 LEU PRO VAL LEU ALA LYS ILE LEU GLU ASP GLU GLU LYS SEQRES 4 A 50 HIS ILE GLU TRP LEU GLU THR ILE LEU GLY NH2 SEQRES 1 B 50 ACE ASP TYR LEU ARG GLU LEU LEU LYS LEU GLU LEU GLN SEQRES 2 B 50 LEU ILE LYS GLN TYR ARG GLU ALA LEU GLU TYR VAL LYS SEQRES 3 B 50 LEU PRO VAL LEU ALA LYS ILE LEU GLU ASP GLU GLU LYS SEQRES 4 B 50 HIS ILE GLU TRP LEU GLU THR ILE LEU GLY NH2
HET ACE A 0 6 HET NH2 A 49 3 HET ACE B 0 6 HET NH2 B 49 3
HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP
FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 NH2 2(H2 N)
HELIX 1 1 LEU A 7 LYS A 25 1 19 HELIX 2 2 LEU A 26 GLU A 44 1 19 HELIX 3 3 ASP B 1 LEU B 7 1 7 HELIX 4 4 LEU B 7 TYR B 23 1 17 HELIX 5 5 LEU B 26 ILE B 46 1 21
LINK C ACE A 0 N ASP A 1 1555 1555 1.34 LINK C GLY A 48 N NH2 A 49 1555 1555 1.33 LINK C ACE B 0 N ASP B 1 1555 1555 1.34 LINK C GLY B 48 N NH2 B 49 1555 1555 1.33
SITE 1 AC3 1 GLY A 48 SITE 1 AC4 1 GLY B 48
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