HEADER CYTOKINE 30-AUG-13 4MID TITLE CRYSTAL STRUCTURE OF ACTIVIN A/BMP2 CHIMERA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AB204 ACTIVIN A/BMP2 CHIMERA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS CYSTEINE KNOT, CYTOKINE, ACTRII, BMPRIA, SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR L.ESQUIVIES REVDAT 4 17-JUL-19 4MID 1 REMARK REVDAT 3 15-NOV-17 4MID 1 REMARK REVDAT 2 03-SEP-14 4MID 1 JRNL REVDAT 1 07-MAY-14 4MID 0 JRNL AUTH B.H.YOON,L.ESQUIVIES,C.AHN,P.C.GRAY,S.K.YE,W.KWIATKOWSKI, JRNL AUTH 2 S.CHOE JRNL TITL AN ACTIVIN A/BMP2 CHIMERA, AB204, DISPLAYS BONE-HEALING JRNL TITL 2 PROPERTIES SUPERIOR TO THOSE OF BMP2. JRNL REF J.BONE MINER.RES. V. 29 1950 2014 JRNL REFN ISSN 0884-0431 JRNL PMID 24692083 JRNL DOI 10.1002/JBMR.2238 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 5342 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.570 REMARK 3 FREE R VALUE TEST SET COUNT : 244 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 28.2479 - 2.6944 1.00 2714 130 0.2145 0.2537 REMARK 3 2 2.6944 - 2.1388 0.92 2384 114 0.2361 0.3113 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.97000 REMARK 3 B22 (A**2) : 11.97000 REMARK 3 B33 (A**2) : -23.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.003 847 REMARK 3 ANGLE : 0.767 1147 REMARK 3 CHIRALITY : 0.048 125 REMARK 3 PLANARITY : 0.005 149 REMARK 3 DIHEDRAL : 14.453 310 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 10 THROUGH 44 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.9813 7.6733 -15.3923 REMARK 3 T TENSOR REMARK 3 T11: 0.3544 T22: 0.2233 REMARK 3 T33: 0.2522 T12: 0.0219 REMARK 3 T13: -0.0204 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 4.4545 L22: 4.2672 REMARK 3 L33: 6.4494 L12: 0.8492 REMARK 3 L13: -1.4354 L23: -2.1968 REMARK 3 S TENSOR REMARK 3 S11: 0.3743 S12: 0.0762 S13: -0.4557 REMARK 3 S21: -0.1551 S22: 0.1698 S23: 0.2182 REMARK 3 S31: 0.9441 S32: 0.1439 S33: -0.3431 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 45 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.6168 6.8300 10.4814 REMARK 3 T TENSOR REMARK 3 T11: 0.4808 T22: 0.3024 REMARK 3 T33: 0.3764 T12: -0.0074 REMARK 3 T13: -0.1495 T23: 0.0749 REMARK 3 L TENSOR REMARK 3 L11: 1.6009 L22: 3.7577 REMARK 3 L33: 8.5569 L12: 2.0145 REMARK 3 L13: -0.3840 L23: 0.8690 REMARK 3 S TENSOR REMARK 3 S11: 0.4508 S12: -0.0164 S13: -0.5740 REMARK 3 S21: 0.3239 S22: -0.1480 S23: -0.8508 REMARK 3 S31: 0.6337 S32: 0.3282 S33: -0.2044 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7633 18.3736 -14.9522 REMARK 3 T TENSOR REMARK 3 T11: 0.3355 T22: 0.2121 REMARK 3 T33: 0.2890 T12: 0.0040 REMARK 3 T13: -0.0163 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 2.9771 L22: 4.4341 REMARK 3 L33: 8.7125 L12: 1.7621 REMARK 3 L13: -2.5515 L23: -2.9934 REMARK 3 S TENSOR REMARK 3 S11: 0.0593 S12: -0.0835 S13: 0.3764 REMARK 3 S21: -0.0478 S22: -0.0733 S23: -0.0463 REMARK 3 S31: -0.5935 S32: 0.1452 S33: 0.0427 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4MID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081947. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5395 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.139 REMARK 200 RESOLUTION RANGE LOW (A) : 147.358 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.24800 REMARK 200 R SYM FOR SHELL (I) : 0.24800 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LISO4, 0.1 M TRIS, 30% PEG 4000, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.11933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 98.23867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 98.23867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.11933 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 Y-1,X,-Z 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: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL 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 BIOMT1 2 -0.500000 0.866025 0.000000 -48.92250 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 28.24542 REMARK 350 BIOMT3 2 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 MET A 0 REMARK 465 GLN A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 HIS A 4 REMARK 465 LYS A 5 REMARK 465 GLN A 6 REMARK 465 ARG A 7 REMARK 465 LYS A 8 REMARK 465 ARG A 9 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 OD1 ASP A 44 O HOH A 216 2.17 REMARK 500 OD2 ASP A 22 O HOH A 217 2.17 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 ASN A 41 173.01 60.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CHIMERA SEQUENCE MATCHES TO HUMAN BMP2 P12643 AND HUMAN ACTIVIN/ REMARK 999 INHIBIN A CHAIN. MATCHING TO THE ABOVE TWO ARE NOT DISTINCTLY REMARK 999 SEPARATED AT ANY CERTAIN RESIDUE THUS NO DBREF IS GIVEN. DBREF 4MID A 0 114 PDB 4MID 4MID 0 114 SEQRES 1 A 115 MET GLN ALA LYS HIS LYS GLN ARG LYS ARG LEU LYS SER SEQRES 2 A 115 SER CYS LYS ARG HIS PRO LEU TYR VAL ASP PHE SER ASP SEQRES 3 A 115 VAL GLY TRP ASN ASP TRP ILE ILE ALA PRO SER GLY TYR SEQRES 4 A 115 HIS ALA ASN TYR CYS ASP GLY GLU CYS PRO PHE PRO LEU SEQRES 5 A 115 ALA ASP HIS LEU ASN SER THR ASN HIS ALA ILE VAL GLN SEQRES 6 A 115 THR LEU VAL ASN SER VAL ASN SER LYS ILE PRO LYS ALA SEQRES 7 A 115 CYS CYS VAL PRO THR LYS LEU ARG PRO MET SER MET LEU SEQRES 8 A 115 TYR TYR ASP ASP GLY GLN ASN ILE ILE LYS LYS ASP ILE SEQRES 9 A 115 GLN ASN MET ILE VAL GLU GLU CYS GLY CYS SER FORMUL 2 HOH *20(H2 O) HELIX 1 1 ALA A 52 ASN A 56 5 5 HELIX 2 2 THR A 58 ASN A 71 1 14 SHEET 1 A 2 LYS A 15 HIS A 17 0 SHEET 2 A 2 TYR A 42 ASP A 44 -1 O TYR A 42 N HIS A 17 SHEET 1 B 2 TYR A 20 ASP A 22 0 SHEET 2 B 2 GLY A 37 HIS A 39 -1 O TYR A 38 N VAL A 21 SHEET 1 C 3 ILE A 32 ALA A 34 0 SHEET 2 C 3 CYS A 78 TYR A 92 -1 O LEU A 90 N ALA A 34 SHEET 3 C 3 ILE A 98 SER A 114 -1 O ILE A 99 N TYR A 91 SSBOND 1 CYS A 78 CYS A 78 1555 4465 2.03 SSBOND 2 CYS A 79 CYS A 14 1555 1555 2.03 SSBOND 3 CYS A 111 CYS A 43 1555 1555 2.03 SSBOND 4 CYS A 113 CYS A 47 1555 1555 2.03 CISPEP 1 ALA A 34 PRO A 35 0 -0.68 CISPEP 2 PHE A 49 PRO A 50 0 7.30 CRYST1 32.615 32.615 147.358 90.00 90.00 120.00 P 31 2 1 6 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 0.030661 0.017702 0.000000 0.00000 SCALE2 0.000000 0.035404 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006786 0.00000