HEADER HYDROLASE INHIBITOR 15-NOV-07 2JXD TITLE NMR STRUCTURE OF HUMAN SERINE PROTEASE INHIBITOR KAZAL TYPE TITLE 2 II (SPINK2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE PROTEASE INHIBITOR KAZAL-TYPE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KAZAL-TYPE DOMAIN; COMPND 5 SYNONYM: ACROSIN-TRYPSIN INHIBITOR, HUSI-II; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SPINK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET32A KEYWDS ANTI-PARALLEL BETA SHEET, BETA-BULGE, DISULFIDE BOND, ALPHA KEYWDS 2 HELIX, PROTEASE INHIBITOR, PYRROLIDONE CARBOXYLIC ACID, KEYWDS 3 SECRETED, SERINE PROTEASE INHIBITOR, HYDROLASE INHIBITOR EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR T.CHEN,T.-R.LEE,P.-C.LYU REVDAT 3 09-FEB-10 2JXD 1 JRNL REVDAT 2 24-FEB-09 2JXD 1 VERSN REVDAT 1 18-NOV-08 2JXD 0 JRNL AUTH T.CHEN,T.-R.LEE,W.-G.LIANG,W.-S.W.CHANG,P.-C.LYU JRNL TITL IDENTIFICATION OF TRYPSIN-INHIBITORY SITE AND JRNL TITL 2 STRUCTURE DETERMINATION OF HUMAN SPINK2 SERINE JRNL TITL 3 PROTEINASE INHIBITOR JRNL REF PROTEINS V. 77 209 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 19422058 JRNL DOI 10.1002/PROT.22432 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER A.T. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATIONS WERE CARRIED REMARK 3 OUT WITH THE STANDARD SIMULATED ANNEALING PROTOCOL BY USING REMARK 3 THE CNS 1.1 PROGRAM. SEVERAL ROUNDS OF CALCULATIONS WERE USED REMARK 3 TO ELIMINATE THE AMBIGUITY IN THE ASSIGNMENT.FINAL STRUCTURES REMARK 3 WERE REFINED BY THE EXPLICIT WATER MODEL USING THE OPLS FORCE REMARK 3 FIELD IN RECOORD AND EVALUATED WITH PROCHECK-NMR. REMARK 4 REMARK 4 2JXD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-07. REMARK 100 THE RCSB ID CODE IS RCSB100409. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM SPINK2, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY 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 : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, WATER REMARK 210 REFINEMENT 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: 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: 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 LEU A 43 H ILE A 47 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 1 LEU A 43 C LEU A 43 O -0.144 REMARK 500 2 LEU A 43 C LEU A 43 O -0.123 REMARK 500 3 LEU A 43 C LEU A 43 O -0.139 REMARK 500 4 LEU A 43 C LEU A 43 O -0.118 REMARK 500 5 LEU A 43 C LEU A 43 O -0.139 REMARK 500 6 LEU A 43 C LEU A 43 O -0.118 REMARK 500 7 LEU A 43 C LEU A 43 O -0.124 REMARK 500 8 LEU A 43 C LEU A 43 O -0.143 REMARK 500 9 LEU A 43 C LEU A 43 O -0.121 REMARK 500 10 LEU A 43 C LEU A 43 O -0.123 REMARK 500 11 LEU A 43 C LEU A 43 O -0.131 REMARK 500 12 LEU A 43 C LEU A 43 O -0.149 REMARK 500 13 LEU A 43 C LEU A 43 O -0.142 REMARK 500 14 LEU A 43 C LEU A 43 O -0.136 REMARK 500 15 LEU A 43 C LEU A 43 O -0.135 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 37 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 5 TYR A 37 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 12 TYR A 37 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 14 TYR A 37 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 PHE A 3 -47.56 70.58 REMARK 500 1 LYS A 8 -67.01 77.26 REMARK 500 1 TYR A 9 -161.33 173.63 REMARK 500 1 TYR A 17 33.41 70.38 REMARK 500 1 ARG A 24 175.54 63.89 REMARK 500 1 MET A 34 65.48 62.55 REMARK 500 1 SER A 35 111.30 -160.65 REMARK 500 1 ALA A 38 92.94 152.47 REMARK 500 1 ASN A 39 -178.11 174.04 REMARK 500 1 THR A 42 -64.09 -93.09 REMARK 500 1 GLU A 49 20.97 -179.38 REMARK 500 2 TYR A 9 -155.74 70.96 REMARK 500 2 ARG A 18 148.92 81.59 REMARK 500 2 ARG A 24 -76.14 -69.08 REMARK 500 2 ASN A 27 80.40 -157.02 REMARK 500 2 MET A 34 -61.00 -176.53 REMARK 500 2 ALA A 38 -36.57 178.56 REMARK 500 2 GLU A 40 21.01 -79.22 REMARK 500 2 THR A 42 -68.26 -122.53 REMARK 500 3 PHE A 3 -41.30 71.80 REMARK 500 3 TYR A 9 -161.62 63.14 REMARK 500 3 TYR A 17 122.54 -171.93 REMARK 500 3 LEU A 19 101.55 82.73 REMARK 500 3 HIS A 25 71.67 82.98 REMARK 500 3 MET A 34 74.26 65.02 REMARK 500 3 SER A 35 102.19 179.76 REMARK 500 3 ALA A 38 87.63 152.73 REMARK 500 3 THR A 42 -60.89 -105.82 REMARK 500 3 GLU A 49 34.87 -179.31 REMARK 500 4 GLN A 2 -61.44 -96.97 REMARK 500 4 PHE A 6 -61.55 72.91 REMARK 500 4 LYS A 8 127.46 56.20 REMARK 500 4 TYR A 9 -149.18 -132.18 REMARK 500 4 CYS A 14 31.14 -79.59 REMARK 500 4 ARG A 24 143.50 70.97 REMARK 500 4 MET A 34 87.64 62.74 REMARK 500 4 SER A 35 110.32 172.75 REMARK 500 4 ALA A 38 98.44 149.08 REMARK 500 4 ASN A 39 173.83 168.43 REMARK 500 4 THR A 42 -63.52 -97.36 REMARK 500 4 GLU A 49 22.69 169.70 REMARK 500 5 PHE A 3 -36.94 -142.03 REMARK 500 5 PHE A 6 152.46 74.70 REMARK 500 5 SER A 7 -84.38 61.18 REMARK 500 5 TYR A 9 -157.22 64.38 REMARK 500 5 HIS A 25 92.05 -171.36 REMARK 500 5 PHE A 26 147.64 -172.19 REMARK 500 5 ASP A 33 36.32 -82.71 REMARK 500 5 ALA A 38 105.85 155.49 REMARK 500 5 ASN A 39 -174.24 166.73 REMARK 500 REMARK 500 THIS ENTRY HAS 158 RAMACHANDRAN OUTLIERS. 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 ARG A 10 0.09 SIDE CHAIN REMARK 500 2 ARG A 10 0.16 SIDE CHAIN REMARK 500 3 ARG A 10 0.07 SIDE CHAIN REMARK 500 5 ARG A 10 0.08 SIDE CHAIN REMARK 500 10 ARG A 10 0.09 SIDE CHAIN REMARK 500 15 ARG A 10 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 4 LYS A 8 25.0 L L OUTSIDE RANGE REMARK 500 6 GLN A 2 22.3 L L OUTSIDE RANGE REMARK 500 7 ASN A 39 23.6 L L OUTSIDE RANGE REMARK 500 7 CYS A 44 16.0 L L OUTSIDE RANGE REMARK 500 9 ARG A 58 24.8 L L OUTSIDE RANGE REMARK 500 10 CYS A 44 22.1 L L OUTSIDE RANGE REMARK 500 11 ASN A 39 24.5 L L OUTSIDE RANGE REMARK 500 14 CYS A 44 24.5 L L OUTSIDE RANGE REMARK 500 15 ARG A 58 20.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL DBREF 2JXD A 1 62 UNP P20155 ISK2_HUMAN 23 84 SEQRES 1 A 62 PRO GLN PHE GLY LEU PHE SER LYS TYR ARG THR PRO ASN SEQRES 2 A 62 CYS SER GLN TYR ARG LEU PRO GLY CYS PRO ARG HIS PHE SEQRES 3 A 62 ASN PRO VAL CYS GLY SER ASP MET SER THR TYR ALA ASN SEQRES 4 A 62 GLU CYS THR LEU CYS MET LYS ILE ARG GLU GLY GLY HIS SEQRES 5 A 62 ASN ILE LYS ILE ILE ARG ASN GLY PRO CYS HELIX 1 1 THR A 42 GLU A 49 1 8 SHEET 1 A 3 THR A 36 TYR A 37 0 SHEET 2 A 3 VAL A 29 GLY A 31 -1 N VAL A 29 O TYR A 37 SHEET 3 A 3 ILE A 56 ARG A 58 -1 O ARG A 58 N CYS A 30 SSBOND 1 CYS A 14 CYS A 44 1555 1555 2.02 SSBOND 2 CYS A 22 CYS A 41 1555 1555 2.01 SSBOND 3 CYS A 30 CYS A 62 1555 1555 2.02 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 233 0 0 1 3 0 0 6 0 0 0 5 END