HEADER SIGNALING PROTEIN 28-SEP-18 6MM2 TITLE CARBON REGULATORY PII-LIKE PROTEIN SBTB FROM CYANOBIUM SP. 7001 BOUND TITLE 2 TO ATP AND CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBON REGULATORY PII-LIKE PROTEIN SBTB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CYANOBIUM SP. PCC 7001; SOURCE 3 ORGANISM_TAXID: 180281; SOURCE 4 GENE: CPCC7001_1671; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETMCSIII KEYWDS PII-LIKE PROTEIN, SBTB, REGULATORY PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.KACZMARSKI,C.JACKSON REVDAT 2 11-OCT-23 6MM2 1 JRNL REVDAT 1 18-SEP-19 6MM2 0 JRNL AUTH C.JACKSON,J.A.KACZMARSKI,D.PRICE JRNL TITL STRUCTURE AND FUNCTION OF SBTB FROM CYANOBIUM SP. 7001 JRNL REF BIORXIV 2019 JRNL REFN ISSN 2692-8205 REMARK 2 REMARK 2 RESOLUTION. 1.04 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 44104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 1.0760 - 1.0400 0.65 0 0 0.3543 0.4062 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6MM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44144 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 16.045 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.9990 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 1.33700 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5O3P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % 2-METHYL-2,4-PENTANEDIOL 0.02 M REMARK 280 CALCIUM CHLORIDE 0.1 M SODIUM ACETATE-ACETIC ACID PH 4.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.02900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.02785 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.73800 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 26.02900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 15.02785 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.73800 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 26.02900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 15.02785 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.73800 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.05570 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 63.47600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.05570 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 63.47600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.05570 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 63.47600 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.0 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 52.05800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 26.02900 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 45.08355 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 365 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 384 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 390 LIES ON A SPECIAL POSITION. 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 ARG A 100 REMARK 465 ALA A 101 REMARK 465 HIS A 102 REMARK 465 LYS A 103 REMARK 465 PHE A 104 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 89 133.18 -174.11 REMARK 500 CYS A 89 131.40 -174.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 41 O REMARK 620 2 ASN A 44 OD1 95.0 REMARK 620 3 GLU A 50 OE1 152.1 92.9 REMARK 620 4 GLU A 50 OE2 154.2 94.0 50.8 REMARK 620 5 ATP A 201 O1G 85.1 159.8 96.4 78.3 REMARK 620 6 ATP A 201 O2B 76.6 83.2 130.9 80.5 77.2 REMARK 620 7 HOH A 349 O 82.0 112.2 70.3 116.5 87.9 154.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 DBREF 6MM2 A 2 104 UNP B5II98 B5II98_9CYAN 2 104 SEQADV 6MM2 SER A 1 UNP B5II98 EXPRESSION TAG SEQRES 1 A 104 SER SER GLN GLN VAL TRP LYS LEU VAL ILE ILE THR GLU SEQRES 2 A 104 GLU ILE LEU LEU LYS LYS VAL SER LYS ILE ILE LYS GLU SEQRES 3 A 104 ALA GLY ALA SER GLY TYR THR VAL LEU ALA ALA ALA GLY SEQRES 4 A 104 GLU GLY SER ARG ASN VAL ARG SER THR GLY GLU PRO SER SEQRES 5 A 104 VAL SER HIS ALA TYR SER ASN ILE LYS PHE GLU VAL LEU SEQRES 6 A 104 THR ALA SER ARG GLU LEU ALA ASP GLN ILE GLN ASP LYS SEQRES 7 A 104 VAL VAL ALA LYS TYR PHE ASP ASP TYR SER CYS ILE THR SEQRES 8 A 104 TYR ILE SER THR VAL GLU ALA LEU ARG ALA HIS LYS PHE HET ATP A 201 43 HET CA A 202 1 HET CL A 203 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 CA CA 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *111(H2 O) HELIX 1 AA1 LEU A 16 ALA A 27 1 12 HELIX 2 AA2 SER A 68 PHE A 84 1 17 SHEET 1 AA1 4 THR A 33 GLY A 39 0 SHEET 2 AA1 4 TYR A 57 THR A 66 -1 O TYR A 57 N GLY A 39 SHEET 3 AA1 4 GLN A 3 GLU A 13 -1 N ILE A 10 O PHE A 62 SHEET 4 AA1 4 CYS A 89 ALA A 98 -1 O SER A 94 N LYS A 7 LINK O GLY A 41 CA CA A 202 1555 1555 2.36 LINK OD1 ASN A 44 CA CA A 202 1555 1555 2.37 LINK OE1 GLU A 50 CA CA A 202 1555 1555 2.60 LINK OE2 GLU A 50 CA CA A 202 1555 1555 2.49 LINK O1G ATP A 201 CA CA A 202 1555 1555 2.40 LINK O2B ATP A 201 CA CA A 202 1555 1555 2.33 LINK CA CA A 202 O HOH A 349 1555 1555 2.49 SITE 1 AC1 24 ILE A 11 SER A 30 GLY A 31 TYR A 32 SITE 2 AC1 24 THR A 33 GLY A 39 GLU A 40 GLY A 41 SITE 3 AC1 24 SER A 42 ARG A 43 ASN A 44 VAL A 45 SITE 4 AC1 24 ARG A 46 GLU A 50 TYR A 57 ASN A 59 SITE 5 AC1 24 GLU A 63 LEU A 65 SER A 88 CYS A 89 SITE 6 AC1 24 ILE A 90 CA A 202 HOH A 313 HOH A 319 SITE 1 AC2 5 GLY A 41 ASN A 44 GLU A 50 ATP A 201 SITE 2 AC2 5 HOH A 349 SITE 1 AC3 1 LYS A 61 CRYST1 52.058 52.058 95.214 90.00 90.00 120.00 H 3 9 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 0.019209 0.011091 0.000000 0.00000 SCALE2 0.000000 0.022181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010503 0.00000