HEADER STRUCTURAL PROTEIN 31-JAN-23 8I74 TITLE CRYSTAL STRUCTURE OF DECARBOXYLATED OSTEOCALCIN AT PH 8.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OSTEOCALCIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BONE GLA PROTEIN,BGP,GAMMA-CARBOXYGLUTAMIC ACID-CONTAINING COMPND 5 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: BGLAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CA-BINDING PROTEIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.YOKOYAMA,Y.NABESHIMA,T.OBITA,M.MIZUGUCHI REVDAT 2 21-AUG-24 8I74 1 JRNL REVDAT 1 31-JAN-24 8I74 0 JRNL AUTH M.MIZUGUCHI,T.YOKOYAMA,T.OTANI,S.KURIBARA,Y.NABESHIMA, JRNL AUTH 2 T.OBITA,M.HIRATA,K.KAWANO JRNL TITL STRUCTURAL AND MUTATIONAL ANALYSES OF DECARBOXYLATED JRNL TITL 2 OSTEOCALCIN PROVIDE INSIGHT INTO ITS ADIPONECTIN-INDUCING JRNL TITL 3 ACTIVITY. JRNL REF FEBS LETT. V. 597 1479 2023 JRNL REFN ISSN 0014-5793 JRNL PMID 36976525 JRNL DOI 10.1002/1873-3468.14618 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14855 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 743 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 30.2630 - 2.3240 0.99 2869 152 0.1851 0.1759 REMARK 3 2 2.3240 - 1.8447 1.00 2813 148 0.1837 0.2236 REMARK 3 3 1.8447 - 1.6115 1.00 2825 148 0.1453 0.1881 REMARK 3 4 1.6115 - 1.4642 1.00 2803 148 0.1529 0.2020 REMARK 3 5 1.4642 - 1.3600 1.00 2802 147 0.1616 0.1774 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.340 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 : 0.006 580 REMARK 3 ANGLE : 0.871 786 REMARK 3 CHIRALITY : 0.070 75 REMARK 3 PLANARITY : 0.005 110 REMARK 3 DIHEDRAL : 26.696 230 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 8I74 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14857 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.110 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 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 : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS-HCL PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.96850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 9.48425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.45275 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 12 REMARK 465 SER A 13 REMARK 465 GLY A 14 REMARK 465 SER A 15 REMARK 465 GLY A 16 REMARK 465 GLY B 12 REMARK 465 SER B 13 REMARK 465 GLY B 14 REMARK 465 SER B 15 REMARK 465 GLY B 16 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 LEU B 25 31.37 -88.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 8I74 A 17 49 UNP P02820 OSTCN_BOVIN 68 100 DBREF 8I74 B 17 49 UNP P02820 OSTCN_BOVIN 68 100 SEQADV 8I74 GLY A 12 UNP P02820 EXPRESSION TAG SEQADV 8I74 SER A 13 UNP P02820 EXPRESSION TAG SEQADV 8I74 GLY A 14 UNP P02820 EXPRESSION TAG SEQADV 8I74 SER A 15 UNP P02820 EXPRESSION TAG SEQADV 8I74 GLY A 16 UNP P02820 EXPRESSION TAG SEQADV 8I74 GLY B 12 UNP P02820 EXPRESSION TAG SEQADV 8I74 SER B 13 UNP P02820 EXPRESSION TAG SEQADV 8I74 GLY B 14 UNP P02820 EXPRESSION TAG SEQADV 8I74 SER B 15 UNP P02820 EXPRESSION TAG SEQADV 8I74 GLY B 16 UNP P02820 EXPRESSION TAG SEQRES 1 A 38 GLY SER GLY SER GLY GLU PRO LYS ARG GLU VAL CYS GLU SEQRES 2 A 38 LEU ASN PRO ASP CYS ASP GLU LEU ALA ASP HIS ILE GLY SEQRES 3 A 38 PHE GLN GLU ALA TYR ARG ARG PHE TYR GLY PRO VAL SEQRES 1 B 38 GLY SER GLY SER GLY GLU PRO LYS ARG GLU VAL CYS GLU SEQRES 2 B 38 LEU ASN PRO ASP CYS ASP GLU LEU ALA ASP HIS ILE GLY SEQRES 3 B 38 PHE GLN GLU ALA TYR ARG ARG PHE TYR GLY PRO VAL FORMUL 3 HOH *57(H2 O) HELIX 1 AA1 GLU A 17 ASN A 26 1 10 HELIX 2 AA2 ASN A 26 GLY A 37 1 12 HELIX 3 AA3 GLY A 37 GLY A 47 1 11 HELIX 4 AA4 PRO B 18 LEU B 25 1 8 HELIX 5 AA5 ASN B 26 GLY B 37 1 12 HELIX 6 AA6 GLY B 37 GLY B 47 1 11 SSBOND 1 CYS A 23 CYS A 29 1555 1555 2.04 SSBOND 2 CYS B 23 CYS B 29 1555 1555 2.04 CRYST1 42.799 42.799 37.937 90.00 90.00 90.00 P 41 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 0.023365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023365 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026359 0.00000