HEADER SUGAR BINDING PROTEIN 04-APR-06 2DJM TITLE SOLUTION STRUCTURE OF N-TERMINAL STARCH-BINDING DOMAIN OF GLUCOAMYLASE TITLE 2 FROM RHIZOPUS ORYZAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOAMYLASE A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: STARCH-BINDING DOMAIN, RESDIUES 1-106; COMPND 5 SYNONYM: FAMILY 21 CARBOHYDRATE-BINDING MODULE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOPUS ORYZAE; SOURCE 3 ORGANISM_TAXID: 64495; SOURCE 4 GENE: AMYA; 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: PET23A KEYWDS BETA SANDWICH, ANTI-PARALLEL, STRACH BINDING, CARBOHYDRATE BINDING, KEYWDS 2 SUGAR BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Y.N.LIU,Y.T.LAI,P.C.LYU REVDAT 3 09-MAR-22 2DJM 1 REMARK REVDAT 2 24-FEB-09 2DJM 1 VERSN REVDAT 1 27-MAR-07 2DJM 0 JRNL AUTH Y.N.LIU,Y.T.LAI,W.I.CHOU,M.D.T.CHANG,P.C.LYU JRNL TITL SOLUTION STRUCTURE OF FAMILY 21 CARBOHYDRATE-BINDING MODULE JRNL TITL 2 FROM RHIZOPUS ORYZAE GLUCOAMYLASE JRNL REF BIOCHEM.J. V. 403 21 2007 JRNL REFN ISSN 0264-6021 JRNL PMID 17117925 JRNL DOI 10.1042/BJ20061312 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, ARIA 2.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), NILGES, M., O'DONOGHUE, S.I. REMARK 3 (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2414 RESTRAINTS, 2238 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 102 DIHEDRAL ANGLE RESTRAINTS,74 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 2DJM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025491. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 10MM SODIUM ACETATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM SBD (UNLABEL); 10MM SODIUM REMARK 210 ACTTATE PH4.5; 10% D2O, 90% H2O; REMARK 210 N15 LABEL 1MM SBD; 10MM SODIUM REMARK 210 ACTTATE PH4.5; 10% D2O, 90% H2O; REMARK 210 N15,C13 DOUBLE LABEL 1MM SBD; REMARK 210 10MM SODIUM ACTTATE PH4.5; 10% REMARK 210 D2O, 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY; DQF-COSY; REMARK 210 3D_N15_HSQC_TOCSY; 3D_N15_HSQC_ REMARK 210 NOESY; CBCA(CO)NH; HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, SPARKY 3.111, CNS REMARK 210 1.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, DISTANCE REMARK 210 GEOMETRY, SIMULATED ANNEALING, REMARK 210 WATER REFINE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING BOTH 2D HOMONUCLEAR AND REMARK 210 TRIPLE-RESONANCE NMR SPECTROSCOPY. 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 HG12 ILE A 30 HH TYR A 86 1.25 REMARK 500 H ALA A 41 O GLU A 81 1.60 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 2 TYR A 40 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 LYS A 35 N - CA - CB ANGL. DEV. = -14.8 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 SER A 5 -63.88 -152.77 REMARK 500 1 ALA A 7 -158.20 -150.99 REMARK 500 1 SER A 13 167.25 176.55 REMARK 500 1 ASP A 17 126.14 -179.76 REMARK 500 1 ALA A 31 -151.86 -125.43 REMARK 500 1 ASP A 45 91.26 76.58 REMARK 500 1 ASN A 46 154.64 84.69 REMARK 500 1 LYS A 80 -42.07 -147.56 REMARK 500 1 SER A 89 31.95 -77.01 REMARK 500 1 ASN A 96 87.45 -151.93 REMARK 500 1 ASN A 97 -68.20 42.22 REMARK 500 1 ASN A 98 -49.60 -159.92 REMARK 500 1 SER A 99 20.31 -174.48 REMARK 500 1 ALA A 100 -87.31 -129.15 REMARK 500 2 SER A 13 166.52 177.32 REMARK 500 2 ASP A 17 117.82 -174.71 REMARK 500 2 ALA A 31 -86.40 -101.49 REMARK 500 2 TYR A 32 -68.47 -163.77 REMARK 500 2 ASN A 46 140.28 -173.86 REMARK 500 2 ASN A 52 76.30 59.83 REMARK 500 2 ASN A 66 55.01 -95.43 REMARK 500 2 ASN A 96 31.98 -144.03 REMARK 500 2 ASN A 97 -67.60 67.88 REMARK 500 2 ASN A 98 40.25 -171.66 REMARK 500 2 ASN A 101 115.10 67.94 REMARK 500 3 SER A 5 -54.96 -128.44 REMARK 500 3 SER A 6 -68.62 -106.09 REMARK 500 3 ALA A 31 -81.18 -103.84 REMARK 500 3 TYR A 32 -73.25 -159.31 REMARK 500 3 ASP A 42 167.22 -40.70 REMARK 500 3 ASP A 45 48.75 74.27 REMARK 500 3 ASN A 49 90.80 -61.71 REMARK 500 3 LYS A 80 -45.86 -139.66 REMARK 500 3 ASN A 97 -33.58 71.83 REMARK 500 3 ASN A 98 -59.55 171.42 REMARK 500 3 SER A 99 26.95 -160.25 REMARK 500 3 ALA A 100 -92.10 -139.10 REMARK 500 4 SER A 5 -66.70 -145.61 REMARK 500 4 ASP A 17 121.94 -172.85 REMARK 500 4 ALA A 31 -156.13 -127.05 REMARK 500 4 ASP A 42 -95.42 6.53 REMARK 500 4 SER A 44 -60.75 -109.60 REMARK 500 4 ASP A 45 38.28 175.46 REMARK 500 4 ASN A 49 -55.61 69.07 REMARK 500 4 ASN A 50 -72.34 -124.83 REMARK 500 4 ASN A 96 -43.35 -139.31 REMARK 500 4 ASN A 97 -45.18 159.82 REMARK 500 4 ASN A 98 -65.06 168.15 REMARK 500 4 SER A 99 51.18 -158.97 REMARK 500 4 ALA A 100 -31.74 -137.36 REMARK 500 REMARK 500 THIS ENTRY HAS 191 RAMACHANDRAN OUTLIERS. 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 SER A 33 LYS A 34 15 -148.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 2DJM A 1 106 GB 82491809 ABB77799 26 131 SEQADV 2DJM ILE A 53 GB 82491809 THR 78 SEE REMARK 999 SEQRES 1 A 106 ALA SER ILE PRO SER SER ALA SER VAL GLN LEU ASP SER SEQRES 2 A 106 TYR ASN TYR ASP GLY SER THR PHE SER GLY LYS ILE TYR SEQRES 3 A 106 VAL LYS ASN ILE ALA TYR SER LYS LYS VAL THR VAL VAL SEQRES 4 A 106 TYR ALA ASP GLY SER ASP ASN TRP ASN ASN ASN GLY ASN SEQRES 5 A 106 ILE ILE ALA ALA SER PHE SER GLY PRO ILE SER GLY SER SEQRES 6 A 106 ASN TYR GLU TYR TRP THR PHE SER ALA SER VAL LYS GLY SEQRES 7 A 106 ILE LYS GLU PHE TYR ILE LYS TYR GLU VAL SER GLY LYS SEQRES 8 A 106 THR TYR TYR ASP ASN ASN ASN SER ALA ASN TYR GLN VAL SEQRES 9 A 106 SER THR SHEET 1 A 4 VAL A 9 TYR A 16 0 SHEET 2 A 4 PHE A 21 VAL A 27 -1 O LYS A 24 N SER A 13 SHEET 3 A 4 GLU A 68 ALA A 74 -1 O ALA A 74 N PHE A 21 SHEET 4 A 4 SER A 57 PRO A 61 -1 N SER A 59 O TYR A 69 SHEET 1 B 4 ILE A 53 ALA A 55 0 SHEET 2 B 4 LYS A 34 ASP A 42 -1 N VAL A 38 O ILE A 54 SHEET 3 B 4 ILE A 79 VAL A 88 -1 O GLU A 87 N LYS A 35 SHEET 4 B 4 THR A 92 ASP A 95 -1 O ASP A 95 N ILE A 84 SHEET 1 C 4 ILE A 53 ALA A 55 0 SHEET 2 C 4 LYS A 34 ASP A 42 -1 N VAL A 38 O ILE A 54 SHEET 3 C 4 ILE A 79 VAL A 88 -1 O GLU A 87 N LYS A 35 SHEET 4 C 4 TYR A 102 GLN A 103 -1 O TYR A 102 N PHE A 82 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