HEADER STRUCTURAL PROTEIN 26-AUG-14 4UXM TITLE CRYSTAL STRUCTURE OF STRUTHIOCALCIN-1, A DIFFERENT CRYSTAL FORM. CAVEAT 4UXM BE7 A 1133 HAS LONG BOND BETWEEN C5 AND HG BE7 A 1133 HAS CAVEAT 2 4UXM LONG BOND BETWEEN HG AND CL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STRUTHIOCALCIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SCA-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STRUTHIO CAMELUS; SOURCE 3 ORGANISM_COMMON: AFRICAN OSTRICH; SOURCE 4 ORGANISM_TAXID: 8801; SOURCE 5 OTHER_DETAILS: EGGSHELL OF OSTRICH KEYWDS STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.R.RUIZ-ARELLANO,A.MORENO,A.ROMERO REVDAT 4 28-FEB-24 4UXM 1 REMARK REVDAT 3 04-APR-18 4UXM 1 REMARK REVDAT 2 22-APR-15 4UXM 1 JRNL REVDAT 1 08-APR-15 4UXM 0 JRNL AUTH R.R.RUIZ-ARELLANO,F.J.MEDRANO,A.MORENO,A.ROMERO JRNL TITL CRYSTAL STRUCTURE OF STRUTHIOCALCIN-1, AN INTRAMINERAL JRNL TITL 2 PROTEIN FROM STRUTHIO CAMELUS EGGSHELL, IN TWO DIFFERENT JRNL TITL 3 CRYSTAL FORMS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 809 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25849392 JRNL DOI 10.1107/S139900471500125X REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1119 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 44.1924 - 2.9998 1.00 2757 144 0.1965 0.2103 REMARK 3 2 2.9998 - 2.3810 1.00 2603 152 0.1962 0.2354 REMARK 3 3 2.3810 - 2.0801 1.00 2573 144 0.1857 0.2009 REMARK 3 4 2.0801 - 1.8899 1.00 2577 144 0.1805 0.2098 REMARK 3 5 1.8899 - 1.7544 1.00 2552 127 0.1791 0.1910 REMARK 3 6 1.7544 - 1.6510 1.00 2551 133 0.1699 0.2075 REMARK 3 7 1.6510 - 1.5683 1.00 2525 147 0.1706 0.2229 REMARK 3 8 1.5683 - 1.5000 1.00 2541 128 0.1867 0.2228 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.16 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 : 0.017 1136 REMARK 3 ANGLE : 1.605 1533 REMARK 3 CHIRALITY : 0.042 141 REMARK 3 PLANARITY : 0.005 196 REMARK 3 DIHEDRAL : 14.532 393 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 4UXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1290061604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0056 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21799 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 44.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 15.40 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 7.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 44.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : 0.09000 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: SAD REMARK 200 SOFTWARE USED: CRANK REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % W/V MPD, 5 % W/V PEG 4000, 100 MM REMARK 280 IMIDAZOLE-HCL PH 8.0.(A4JB7) 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 16.33500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.03000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.95500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.03000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.33500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.95500 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: 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 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 ASP A 1 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 HOH A 2065 O HOH A 2128 2.15 REMARK 500 OH TYR A 59 O HOH A 2009 2.17 REMARK 500 OD1 ASP A 118 O HOH A 2126 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 64 O HOH A 2112 1455 2.16 REMARK 500 NH2 ARG A 26 O9 BE7 A 1133 4456 2.18 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 ASP A 94 69.23 62.10 REMARK 500 ASP A 96 63.37 -66.20 REMARK 500 PRO A 98 35.72 -97.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2028 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A2065 DISTANCE = 5.98 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BE7 A 1133 DBREF 4UXM A 1 132 UNP P83514 SCAL1_STRCA 1 132 SEQRES 1 A 132 ASP LYS CYS PRO LYS GLY TRP LEU ASP PHE ARG GLY ASN SEQRES 2 A 132 CYS TYR GLY TYR PHE ARG TYR GLU LEU PRO TRP LYS ARG SEQRES 3 A 132 ALA GLU ALA TRP CYS ARG SER ILE ARG ALA GLY ALA HIS SEQRES 4 A 132 LEU ALA SER ILE HIS THR SER GLU GLU HIS ARG ALA ILE SEQRES 5 A 132 ALA LYS PHE ILE SER GLN TYR HIS HIS GLY GLU GLU GLU SEQRES 6 A 132 GLU ASP VAL TRP ILE GLY LEU PHE ARG TRP ASN SER VAL SEQRES 7 A 132 TRP ALA TRP ILE ASP GLY SER LYS LYS HIS TYR SER ALA SEQRES 8 A 132 LEU ASP ASP ASP ASP TYR PRO LYS GLY LYS HIS CYS ALA SEQRES 9 A 132 VAL LEU ASP GLU SER SER GLY PHE LEU SER TRP ASP ASN SEQRES 10 A 132 ASP SER CYS GLY GLU ARG ASN ALA PHE ILE CYS LYS CYS SEQRES 11 A 132 THR ALA HET BE7 A1133 11 HETNAM BE7 (4-CARBOXYPHENYL)(CHLORO)MERCURY HETSYN BE7 P-CHLOROMERCURIBENZOIC ACID FORMUL 2 BE7 C7 H5 CL HG O2 FORMUL 3 HOH *132(H2 O) HELIX 1 1 PRO A 23 ARG A 35 1 13 HELIX 2 2 THR A 45 GLN A 58 1 14 HELIX 3 3 GLU A 108 GLY A 111 5 4 SHEET 1 AA 5 LEU A 8 PHE A 10 0 SHEET 2 AA 5 ASN A 13 LEU A 22 -1 O ASN A 13 N PHE A 10 SHEET 3 AA 5 ASN A 124 THR A 131 -1 O ASN A 124 N LEU A 22 SHEET 4 AA 5 VAL A 68 TRP A 75 1 O TRP A 69 N ILE A 127 SHEET 5 AA 5 VAL A 78 TRP A 81 -1 O VAL A 78 N TRP A 75 SHEET 1 AB 4 LEU A 8 PHE A 10 0 SHEET 2 AB 4 ASN A 13 LEU A 22 -1 O ASN A 13 N PHE A 10 SHEET 3 AB 4 ASN A 124 THR A 131 -1 O ASN A 124 N LEU A 22 SHEET 4 AB 4 HIS A 39 LEU A 40 -1 O HIS A 39 N LYS A 129 SHEET 1 AC 2 VAL A 78 TRP A 81 0 SHEET 2 AC 2 VAL A 68 TRP A 75 -1 O PHE A 73 N ALA A 80 SHEET 1 AD 6 LEU A 8 PHE A 10 0 SHEET 2 AD 6 ASN A 13 LEU A 22 -1 O ASN A 13 N PHE A 10 SHEET 3 AD 6 ASN A 124 THR A 131 -1 O ASN A 124 N LEU A 22 SHEET 4 AD 6 VAL A 68 TRP A 75 1 O TRP A 69 N ILE A 127 SHEET 5 AD 6 CYS A 103 LEU A 106 1 O ALA A 104 N ILE A 70 SHEET 6 AD 6 TRP A 115 ASP A 118 1 O ASP A 116 N VAL A 105 SSBOND 1 CYS A 3 CYS A 14 1555 1555 2.04 SSBOND 2 CYS A 31 CYS A 128 1555 1555 2.03 SSBOND 3 CYS A 103 CYS A 120 1555 1555 2.03 SITE 1 AC1 9 LEU A 22 ARG A 26 ARG A 35 ALA A 36 SITE 2 AC1 9 CYS A 130 THR A 131 ALA A 132 HOH A2042 SITE 3 AC1 9 HOH A2059 CRYST1 32.670 55.910 72.060 90.00 90.00 90.00 P 21 21 21 4 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 0.030609 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013877 0.00000