HEADER TRANSCRIPTION 23-OCT-13 4NBO TITLE HUMAN STEROID RECEPTOR RNA ACTIVATOR PROTEIN CARBOXY-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROID RECEPTOR RNA ACTIVATOR 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 106-215; COMPND 5 SYNONYM: STEROID RECEPTOR RNA ACTIVATOR PROTEIN, SRAP; 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: PP7684, SRA, SRA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS 5-HELIX BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR D.B.MCKAY,L.XI,K.K.B.BARTHEL,T.C.CECH REVDAT 3 20-SEP-23 4NBO 1 SEQADV REVDAT 2 08-OCT-14 4NBO 1 JRNL REVDAT 1 05-FEB-14 4NBO 0 JRNL AUTH D.B.MCKAY,L.XI,K.K.BARTHEL,T.R.CECH JRNL TITL STRUCTURE AND FUNCTION OF STEROID RECEPTOR RNA ACTIVATOR JRNL TITL 2 PROTEIN, THE PROPOSED PARTNER OF SRA NONCODING RNA. JRNL REF J.MOL.BIOL. V. 426 1766 2014 JRNL REFN ISSN 0022-2836 JRNL PMID 24486609 JRNL DOI 10.1016/J.JMB.2014.01.006 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9632 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 479 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 39.4932 - 4.0469 1.00 3176 167 0.2264 0.2392 REMARK 3 2 4.0469 - 3.2126 0.99 2996 155 0.2494 0.2907 REMARK 3 3 3.2126 - 2.8066 1.00 2981 157 0.2985 0.3902 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 33.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.880 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) : -0.26010 REMARK 3 B22 (A**2) : -0.26010 REMARK 3 B33 (A**2) : 0.52030 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 : 0.004 1664 REMARK 3 ANGLE : 0.752 2238 REMARK 3 CHIRALITY : 0.038 254 REMARK 3 PLANARITY : 0.002 284 REMARK 3 DIHEDRAL : 17.502 640 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -17.2226 33.8795 -17.7535 REMARK 3 T TENSOR REMARK 3 T11: 0.3651 T22: 0.3185 REMARK 3 T33: 0.3401 T12: -0.0664 REMARK 3 T13: 0.0669 T23: -0.0691 REMARK 3 L TENSOR REMARK 3 L11: 1.9040 L22: 3.4092 REMARK 3 L33: 2.4550 L12: -1.0024 REMARK 3 L13: 0.9596 L23: -0.3697 REMARK 3 S TENSOR REMARK 3 S11: 0.0528 S12: 0.0522 S13: 0.1397 REMARK 3 S21: 0.2240 S22: -0.0224 S23: -0.0545 REMARK 3 S31: -0.1946 S32: 0.2092 S33: -0.0286 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 4NBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000082999. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9695 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29500 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: 2YRU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4-2.0 MALONATE(NA+), 0.1 M MOPS AS REMARK 280 PRECIPITANT, STABILIZED IN 2.4 M MALONATE, 0.1 M MOPS PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 6.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 50.20400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.95050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.95050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.30600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.95050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.95050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.10200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.95050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.95050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.30600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.95050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.95050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.10200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.20400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 105 REMARK 465 GLU A 106 REMARK 465 SER A 107 REMARK 465 GLU A 108 REMARK 465 GLU A 211 REMARK 465 GLU A 212 REMARK 465 ALA A 213 REMARK 465 ALA A 214 REMARK 465 ASN A 215 REMARK 465 MET B 105 REMARK 465 GLU B 106 REMARK 465 SER B 107 REMARK 465 GLU B 108 REMARK 465 GLU B 211 REMARK 465 GLU B 212 REMARK 465 ALA B 213 REMARK 465 ALA B 214 REMARK 465 ASN B 215 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 O VAL B 188 OG SER B 192 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 SER A 210 C - N - CA ANGL. DEV. = 16.8 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 HIS B 187 52.88 -96.23 REMARK 500 SER B 192 42.61 -107.87 REMARK 500 GLN B 193 -43.35 -151.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 4NBO A 106 215 UNP Q9HD15 SRA1_HUMAN 106 215 DBREF 4NBO B 106 215 UNP Q9HD15 SRA1_HUMAN 106 215 SEQADV 4NBO MET A 105 UNP Q9HD15 INITIATING METHIONINE SEQADV 4NBO MET B 105 UNP Q9HD15 INITIATING METHIONINE SEQRES 1 A 111 MET GLU SER GLU ALA VAL MET GLU ASP VAL LEU ARG PRO SEQRES 2 A 111 LEU GLU GLN ALA LEU GLU ASP CYS ARG GLY HIS THR ARG SEQRES 3 A 111 LYS GLN VAL CYS ASP ASP ILE SER ARG ARG LEU ALA LEU SEQRES 4 A 111 LEU GLN GLU GLN TRP ALA GLY GLY LYS LEU SER ILE PRO SEQRES 5 A 111 VAL LYS LYS ARG MET ALA LEU LEU VAL GLN GLU LEU SER SEQRES 6 A 111 SER HIS ARG TRP ASP ALA ALA ASP ASP ILE HIS ARG SER SEQRES 7 A 111 LEU MET VAL ASP HIS VAL THR GLU VAL SER GLN TRP MET SEQRES 8 A 111 VAL GLY VAL LYS ARG LEU ILE ALA GLU LYS ARG SER LEU SEQRES 9 A 111 PHE SER GLU GLU ALA ALA ASN SEQRES 1 B 111 MET GLU SER GLU ALA VAL MET GLU ASP VAL LEU ARG PRO SEQRES 2 B 111 LEU GLU GLN ALA LEU GLU ASP CYS ARG GLY HIS THR ARG SEQRES 3 B 111 LYS GLN VAL CYS ASP ASP ILE SER ARG ARG LEU ALA LEU SEQRES 4 B 111 LEU GLN GLU GLN TRP ALA GLY GLY LYS LEU SER ILE PRO SEQRES 5 B 111 VAL LYS LYS ARG MET ALA LEU LEU VAL GLN GLU LEU SER SEQRES 6 B 111 SER HIS ARG TRP ASP ALA ALA ASP ASP ILE HIS ARG SER SEQRES 7 B 111 LEU MET VAL ASP HIS VAL THR GLU VAL SER GLN TRP MET SEQRES 8 B 111 VAL GLY VAL LYS ARG LEU ILE ALA GLU LYS ARG SER LEU SEQRES 9 B 111 PHE SER GLU GLU ALA ALA ASN HELIX 1 1 VAL A 110 CYS A 125 1 16 HELIX 2 2 ARG A 130 GLY A 151 1 22 HELIX 3 3 SER A 154 SER A 170 1 17 HELIX 4 4 ARG A 172 SER A 192 1 21 HELIX 5 5 TRP A 194 SER A 210 1 17 HELIX 6 6 VAL B 110 ARG B 126 1 17 HELIX 7 7 ARG B 130 GLY B 150 1 21 HELIX 8 8 SER B 154 SER B 170 1 17 HELIX 9 9 ARG B 172 HIS B 187 1 16 HELIX 10 10 TRP B 194 SER B 207 1 14 CRYST1 85.901 85.901 100.408 90.00 90.00 90.00 P 43 21 2 16 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 0.011641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009959 0.00000