HEADER HORMONE 10-MAY-16 5B5I TITLE THE CRYSTAL STRUCTURE OF A CRUSTACEAN HYPERGLYCEMIC HORMONE PRECURSOR TITLE 2 FROM THE KURUMA PRAWN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRUSTACEAN HYPERGLYCEMIC HORMONES 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PEJ-SGP-I; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARSUPENAEUS JAPONICUS; SOURCE 3 ORGANISM_COMMON: KURUMA PRAWN; SOURCE 4 ORGANISM_TAXID: 27405; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRUSTACEA, HYPERGLYCEMIC, HORMONE, NEUROPEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR N.TSUTSUI,K.NAGATA REVDAT 4 26-FEB-20 5B5I 1 REMARK REVDAT 3 21-DEC-16 5B5I 1 JRNL REVDAT 2 26-OCT-16 5B5I 1 JRNL REVDAT 1 19-OCT-16 5B5I 0 JRNL AUTH N.TSUTSUI,T.SAKAMOTO,F.ARISAKA,M.TANOKURA,H.NAGASAWA, JRNL AUTH 2 K.NAGATA JRNL TITL CRYSTAL STRUCTURE OF A CRUSTACEAN HYPERGLYCEMIC HORMONE JRNL TITL 2 (CHH) PRECURSOR SUGGESTS STRUCTURAL VARIETY IN THE JRNL TITL 3 C-TERMINAL REGIONS OF CHH SUPERFAMILY MEMBERS. JRNL REF FEBS J. V. 283 4325 2016 JRNL REFN ISSN 1742-4658 JRNL PMID 27743429 JRNL DOI 10.1111/FEBS.13926 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16354 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 847 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 7.9444 - 2.8676 1.00 2741 121 0.2135 0.2429 REMARK 3 2 2.8676 - 2.2941 1.00 2583 146 0.1954 0.2343 REMARK 3 3 2.2941 - 2.0095 1.00 2562 134 0.1704 0.1696 REMARK 3 4 2.0095 - 1.8282 1.00 2573 137 0.1567 0.1719 REMARK 3 5 1.8282 - 1.6986 1.00 2520 169 0.1482 0.1539 REMARK 3 6 1.6986 - 1.5993 1.00 2528 140 0.1413 0.1482 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1133 REMARK 3 ANGLE : 0.944 1536 REMARK 3 CHIRALITY : 0.048 159 REMARK 3 PLANARITY : 0.005 209 REMARK 3 DIHEDRAL : 19.107 699 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5B5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1300000560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALEPACK REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16354 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8-1.0 M NACL, 50 MM POTASSIUM SODIUM REMARK 280 TARTRATE, 50 MM TARTARIC ACID, 5% ETHANOL, 25% 1,2-ETHANEDIOL, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 19.33950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.89650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.89650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.89650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.33950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.89650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 ALA A 68 REMARK 465 VAL A 69 REMARK 465 GLN A 70 REMARK 465 MET A 71 REMARK 465 VAL A 72 REMARK 465 GLY A 73 REMARK 465 GLY B 0 REMARK 465 VAL B 69 REMARK 465 GLN B 70 REMARK 465 MET B 71 REMARK 465 VAL B 72 REMARK 465 GLY B 73 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OE2 GLU A 67 NE2 GLN B 14 1.94 REMARK 500 O HOH B 104 O HOH B 107 2.17 REMARK 500 O HOH B 102 O HOH B 105 2.18 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 MET A 53 CG - SD - CE ANGL. DEV. = -11.6 DEGREES REMARK 500 MET B 53 CG - SD - CE ANGL. DEV. = -12.8 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 CYS A 7 108.94 -166.70 REMARK 500 CYS B 7 107.21 -166.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 101 DBREF 5B5I A 1 73 UNP O15980 CHH1_PENJP 47 119 DBREF 5B5I B 1 73 UNP O15980 CHH1_PENJP 47 119 SEQADV 5B5I GLY A 0 UNP O15980 EXPRESSION TAG SEQADV 5B5I GLY B 0 UNP O15980 EXPRESSION TAG SEQRES 1 A 74 GLY SER LEU PHE ASP PRO SER CYS THR GLY VAL PHE ASP SEQRES 2 A 74 ARG GLN LEU LEU ARG ARG LEU GLY ARG VAL CYS ASP ASP SEQRES 3 A 74 CYS PHE ASN VAL PHE ARG GLU PRO ASN VAL ALA THR GLU SEQRES 4 A 74 CYS ARG SER ASN CYS TYR ASN ASN PRO VAL PHE ARG GLN SEQRES 5 A 74 CYS MET ALA TYR VAL VAL PRO ALA HIS LEU HIS ASN GLU SEQRES 6 A 74 HIS ARG GLU ALA VAL GLN MET VAL GLY SEQRES 1 B 74 GLY SER LEU PHE ASP PRO SER CYS THR GLY VAL PHE ASP SEQRES 2 B 74 ARG GLN LEU LEU ARG ARG LEU GLY ARG VAL CYS ASP ASP SEQRES 3 B 74 CYS PHE ASN VAL PHE ARG GLU PRO ASN VAL ALA THR GLU SEQRES 4 B 74 CYS ARG SER ASN CYS TYR ASN ASN PRO VAL PHE ARG GLN SEQRES 5 B 74 CYS MET ALA TYR VAL VAL PRO ALA HIS LEU HIS ASN GLU SEQRES 6 B 74 HIS ARG GLU ALA VAL GLN MET VAL GLY HET EOH A 101 3 HETNAM EOH ETHANOL FORMUL 3 EOH C2 H6 O FORMUL 4 HOH *26(H2 O) HELIX 1 AA1 ASP A 12 PHE A 27 1 16 HELIX 2 AA2 GLU A 32 SER A 41 1 10 HELIX 3 AA3 ASN A 42 ASN A 45 5 4 HELIX 4 AA4 ASN A 46 HIS A 62 1 17 HELIX 5 AA5 ASP B 12 PHE B 27 1 16 HELIX 6 AA6 GLU B 32 SER B 41 1 10 HELIX 7 AA7 ASN B 42 ASN B 45 5 4 HELIX 8 AA8 ASN B 46 HIS B 62 1 17 SSBOND 1 CYS A 7 CYS A 43 1555 1555 2.03 SSBOND 2 CYS A 23 CYS A 39 1555 1555 2.05 SSBOND 3 CYS A 26 CYS A 52 1555 1555 2.03 SSBOND 4 CYS B 7 CYS B 43 1555 1555 2.01 SSBOND 5 CYS B 23 CYS B 39 1555 1555 2.03 SSBOND 6 CYS B 26 CYS B 52 1555 1555 2.06 SITE 1 AC1 2 CYS A 43 VAL B 57 CRYST1 38.679 55.793 55.793 90.00 90.00 90.00 P 21 21 21 8 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 0.025854 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017923 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017923 0.00000