10 20 30 40 50 60 70 80 1N9J - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE INHIBITOR 25-NOV-02 1N9J
TITLE SOLUTION STRUCTURE OF THE 3D DOMAIN SWAPPED DIMER OF STEFIN TITLE 2 A
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATIN A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: STEFIN A, CYSTATIN AS; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A
KEYWDS DOMAIN SWAPPED, STEFIN A, CYSTATINS, AMYLOID, HYDROLASE KEYWDS 2 INHIBITOR
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR R.A.STANIFORTH,S.GIANNINI,L.D.HIGGINS,M.J.CONROY, AUTHOR 2 A.M.HOUNSLOW,R.JERALA,C.J.CRAVEN,J.P.WALTHO
REVDAT 2 24-FEB-09 1N9J 1 VERSN REVDAT 1 25-FEB-03 1N9J 0
JRNL AUTH R.A.STANIFORTH,S.GIANNINI,L.D.HIGGINS,M.J.CONROY, JRNL AUTH 2 A.M.HOUNSLOW,R.JERALA,C.J.CRAVEN,J.P.WALTHO JRNL TITL THREE-DIMENSIONAL DOMAIN SWAPPING IN THE FOLDED JRNL TITL 2 AND MOLTEN-GLOBULE STATES OF CYSTATINS, AN JRNL TITL 3 AMYLOID-FORMING STRUCTURAL SUPERFAMILY JRNL REF EMBO J. V. 20 4774 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11532941 JRNL DOI 10.1093/EMBOJ/20.17.4774
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE RESTRAINTS (NOES AND REMARK 3 HYDROGEN BONDS) WERE TAKEN FROM THE DATA USED FOR THE STEFIN A REMARK 3 MONOMER STRUCTURE (MARTIN ET AL., 1995), EXCEPT THOSE REMARK 3 INVOLVING RESIDUES V48-G50 AND N77-L80 WHERE CHEMICAL SHIFT REMARK 3 PERTURBATION WAS OBSERVED FOLLOWING RESONANCE ASSIGNMENT. THE REMARK 3 NOES WERE SPECIFIED AS INTERMOLECULAR AND INTRAMOLECULAR REMARK 3 ACCORDING TO DOMAIN-SWAPPED TOPOLOGY INFERRED FROM ISOTOPE REMARK 3 FILTERING EXPERIMENTS. AN ADDITIONAL HYDROGEN BOND RESTRAINT REMARK 3 WAS INCLUDED BETWEEN 48 AND 50 BASED ON EVIDENCE FROM REMARK 3 PROTECTION EXPERIMENTS ON THE DIMER (JERALA AND ZEROVNIK, REMARK 3 1999). DIHEDRAL RESTRAINTS (PHI AND PSI) WERE DETERMINED USING REMARK 3 THE 1H-ALPHA, 15N, 13C-ALPHA, 13C-BETA AND 13C' CHEMICAL REMARK 3 SHIFTS AND THE PROGRAM TALOS (CORNILESCU ET AL., 1999). WHERE REMARK 3 TALOS GAVE A `POOR' MATCH, THE EXPERIMENTAL PHI DIHEDRAL ANGLE REMARK 3 WAS TAKEN FROM THE DATA USED FOR THE STEFIN A MONOMER REMARK 3 STRUCTURE CALCULATION.
REMARK 4 REMARK 4 1N9J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-02. REMARK 100 THE RCSB ID CODE IS RCSB017687.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2MM STEFIN A U-15N; 50MM REMARK 210 PHOSPHATE BUFFER PH 5.5, 100MM REMARK 210 KCL, 5MM AZIDE; 90% H2O, 10% REMARK 210 D2O; 1MM STEFIN A U-15N,13C, REMARK 210 2H; 50MM PHOSPHATE BUFFER PH REMARK 210 5.5, 100MM KCL, 5MM AZIDE; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA, HNCO, HN(CA)CB, TOCSY- REMARK 210 HSQC, NOESY-HSQC, 15N-ISOTOPE- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 8 CD GLU A 8 OE2 0.109 REMARK 500 GLU A 15 CD GLU A 15 OE2 0.110 REMARK 500 GLU A 18 CD GLU A 18 OE2 0.112 REMARK 500 GLU A 28 CD GLU A 28 OE2 0.109 REMARK 500 GLU A 29 CD GLU A 29 OE2 0.111 REMARK 500 GLU A 33 CD GLU A 33 OE2 0.111 REMARK 500 GLU A 39 CD GLU A 39 OE2 0.111 REMARK 500 GLU A 78 CD GLU A 78 OE2 0.109 REMARK 500 GLU A 94 CD GLU A 94 OE2 0.110 REMARK 500 GLU B 8 CD GLU B 8 OE2 0.109 REMARK 500 GLU B 15 CD GLU B 15 OE2 0.111 REMARK 500 GLU B 18 CD GLU B 18 OE2 0.110 REMARK 500 GLU B 28 CD GLU B 28 OE2 0.101 REMARK 500 GLU B 29 CD GLU B 29 OE2 0.111 REMARK 500 GLU B 33 CD GLU B 33 OE2 0.111 REMARK 500 GLU B 39 CD GLU B 39 OE2 0.106 REMARK 500 GLU B 78 CD GLU B 78 OE2 0.110 REMARK 500 GLU B 94 CD GLU B 94 OE2 0.109 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 21 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 TYR A 35 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 43 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 93 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 HIS B 66 ND1 - CE1 - NE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP B 79 CB - CG - OD1 ANGL. DEV. = 6.0 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 PRO A 11 9.19 -66.47 REMARK 500 ALA A 12 135.72 148.15 REMARK 500 VAL A 41 -141.72 -131.83 REMARK 500 ASP A 61 -29.33 -34.07 REMARK 500 SER A 72 -80.54 -109.56 REMARK 500 TYR A 85 126.89 -172.84 REMARK 500 ASP A 88 4.15 -38.25 REMARK 500 SER B 7 -174.62 -66.81 REMARK 500 PRO B 11 6.37 -66.06 REMARK 500 ALA B 12 74.81 150.26 REMARK 500 VAL B 41 -146.65 -138.56 REMARK 500 VAL B 57 117.29 -162.60 REMARK 500 SER B 72 -91.61 -86.90 REMARK 500 ASP B 88 -8.86 -24.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 58 ALA A 59 134.41 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 ARG A 58 0.31 SIDE_CHAIN REMARK 500 PHE A 98 0.13 SIDE_CHAIN REMARK 500 TYR B 53 0.08 SIDE_CHAIN REMARK 500 TYR B 54 0.08 SIDE_CHAIN REMARK 500 ARG B 58 0.28 SIDE_CHAIN REMARK 500 TYR B 85 0.07 SIDE_CHAIN REMARK 500 PHE B 98 0.10 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DVC RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF MONOMERIC HUMAN STEFIN A AT PH REMARK 900 5.5 AND 308K
DBREF 1N9J A 1 98 UNP P01040 CYTA_HUMAN 1 98 DBREF 1N9J B 1 98 UNP P01040 CYTA_HUMAN 1 98
SEQRES 1 A 98 MET ILE PRO GLY GLY LEU SER GLU ALA LYS PRO ALA THR SEQRES 2 A 98 PRO GLU ILE GLN GLU ILE VAL ASP LYS VAL LYS PRO GLN SEQRES 3 A 98 LEU GLU GLU LYS THR ASN GLU THR TYR GLY LYS LEU GLU SEQRES 4 A 98 ALA VAL GLN TYR LYS THR GLN VAL VAL ALA GLY THR ASN SEQRES 5 A 98 TYR TYR ILE LYS VAL ARG ALA GLY ASP ASN LYS TYR MET SEQRES 6 A 98 HIS LEU LYS VAL PHE LYS SER LEU PRO GLY GLN ASN GLU SEQRES 7 A 98 ASP LEU VAL LEU THR GLY TYR GLN VAL ASP LYS ASN LYS SEQRES 8 A 98 ASP ASP GLU LEU THR GLY PHE SEQRES 1 B 98 MET ILE PRO GLY GLY LEU SER GLU ALA LYS PRO ALA THR SEQRES 2 B 98 PRO GLU ILE GLN GLU ILE VAL ASP LYS VAL LYS PRO GLN SEQRES 3 B 98 LEU GLU GLU LYS THR ASN GLU THR TYR GLY LYS LEU GLU SEQRES 4 B 98 ALA VAL GLN TYR LYS THR GLN VAL VAL ALA GLY THR ASN SEQRES 5 B 98 TYR TYR ILE LYS VAL ARG ALA GLY ASP ASN LYS TYR MET SEQRES 6 B 98 HIS LEU LYS VAL PHE LYS SER LEU PRO GLY GLN ASN GLU SEQRES 7 B 98 ASP LEU VAL LEU THR GLY TYR GLN VAL ASP LYS ASN LYS SEQRES 8 B 98 ASP ASP GLU LEU THR GLY PHE
HELIX 1 1 THR A 13 ASN A 32 1 20 HELIX 2 2 GLN A 76 LEU A 80 5 5 HELIX 3 3 THR B 13 ASN B 32 1 20
SHEET 1 A 2 LYS A 37 ALA A 40 0 SHEET 2 A 2 VAL B 57 GLY B 60 -1 O ARG B 58 N GLU A 39 SHEET 1 B 6 VAL A 81 GLN A 86 0 SHEET 2 B 6 MET A 65 LYS A 71 -1 N PHE A 70 O VAL A 81 SHEET 3 B 6 LYS A 44 ARG A 58 -1 N ILE A 55 O LEU A 67 SHEET 4 B 6 GLU B 39 TYR B 54 -1 O LYS B 44 N TYR A 54 SHEET 5 B 6 LYS B 68 LYS B 71 -1 O LYS B 71 N THR B 51 SHEET 6 B 6 LEU B 80 GLY B 84 -1 O VAL B 81 N PHE B 70
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