1NPS - Header Asymmetric Unit

HEADER SIGNALING PROTEIN 01-FEB-99 1NPS

TITLE CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF PROTEIN S

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEVELOPMENT-SPECIFIC PROTEIN S; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN: MOTIFS 1-2 AND LINKER; COMPND 5 SYNONYM: SPORE COAT PROTEIN S; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYXOCOCCUS XANTHUS; SOURCE 3 ORGANISM_TAXID: 34; SOURCE 4 CELLULAR_LOCATION: CYTOSOL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM

KEYWDS CRYSTALLINE LIKE STRUCTURE, SIGNALING PROTEIN

EXPDTA X-RAY DIFFRACTION

AUTHOR M.WENK,R.BAUMGARTNER,E.M.MAYER,R.HUBER,T.A.HOLAK,R.JAENICKE

REVDAT 3 24-FEB-09 1NPS 1 VERSN REVDAT 2 10-JAN-01 1NPS 1 REMARK REVDAT 1 04-FEB-00 1NPS 0

JRNL AUTH M.WENK,R.BAUMGARTNER,T.A.HOLAK,R.HUBER,R.JAENICKE, JRNL AUTH 2 E.M.MAYR JRNL TITL THE DOMAINS OF PROTEIN S FROM MYXOCOCCUS XANTHUS: JRNL TITL 2 STRUCTURE, STABILITY AND INTERACTIONS. JRNL REF J.MOL.BIOL. V. 286 1533 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10064714 JRNL DOI 10.1006/JMBI.1999.2582

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.BAGBY,T.S.HARVEY,S.G.EAGLE,S.INOUYE,M.IKURA REMARK 1 TITL NMR-DERIVED THREE-DIMENSIONAL SOLUTION STRUCTURE REMARK 1 TITL 2 OF PROTEIN S COMPLEXED WITH CALCIUM REMARK 1 REF STRUCTURE V. 2 107 1994 REMARK 1 REFN ISSN 0969-2126

REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 7166 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : 0.25 REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 662 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 76 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.003 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.900 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1NPS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-99. REMARK 100 THE RCSB ID CODE IS RCSB000438.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 8.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 18.97000 REMARK 290 SMTRY3 2 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 88 O

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 77 23.03 -149.39 REMARK 500 PRO A 87 -65.99 -9.80 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 A 94 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH A 105 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH A 109 DISTANCE = 15.03 ANGSTROMS REMARK 525 HOH A 120 DISTANCE = 5.55 ANGSTROMS REMARK 525 HOH A 126 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 132 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH A 138 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A 147 DISTANCE = 10.43 ANGSTROMS REMARK 525 HOH A 156 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH A 158 DISTANCE = 6.39 ANGSTROMS

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 90 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 7 O REMARK 620 2 SER A 39 OG 86.1 REMARK 620 3 THR A 37 O 90.2 106.1 REMARK 620 4 ASN A 76 OD1 172.3 98.0 82.5 REMARK 620 5 HOH A 166 O 87.8 151.2 102.1 91.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 145 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 77 O REMARK 620 2 SER A 79 OG 112.5 REMARK 620 3 HOH A 93 O 78.0 167.7 REMARK 620 4 GLN A 53 O 76.9 86.2 90.4 REMARK 620 5 HOH A 92 O 159.9 82.1 86.2 91.0 REMARK 620 6 HOH A 99 O 34.4 78.2 112.2 73.7 155.6 REMARK 620 7 ASN A 36 OD1 80.1 91.1 97.1 153.8 114.5 80.3 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 CA A 90 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 145

DBREF 1NPS A 1 88 UNP P02966 DESS_MYXXA 2 89

SEQRES 1 A 88 ALA ASN ILE THR VAL PHE TYR ASN GLU ASP PHE GLN GLY SEQRES 2 A 88 LYS GLN VAL ASP LEU PRO PRO GLY ASN TYR THR ARG ALA SEQRES 3 A 88 GLN LEU ALA ALA LEU GLY ILE GLU ASN ASN THR ILE SER SEQRES 4 A 88 SER VAL LYS VAL PRO PRO GLY VAL LYS ALA ILE LEU TYR SEQRES 5 A 88 GLN ASN ASP GLY PHE ALA GLY ASP GLN ILE GLU VAL VAL SEQRES 6 A 88 ALA ASN ALA GLU GLU LEU GLY PRO LEU ASN ASN ASN VAL SEQRES 7 A 88 SER SER ILE ARG VAL ILE SER VAL PRO VAL

HET CA A 90 1 HET CA A 145 1

HETNAM CA CALCIUM ION

FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *76(H2 O)

HELIX 1 1 ARG A 25 LEU A 31 1 7 HELIX 2 2 GLY A 72 LEU A 74 5 3

SHEET 1 A 3 GLN A 15 LEU A 18 0 SHEET 2 A 3 ILE A 3 PHE A 6 -1 N VAL A 5 O VAL A 16 SHEET 3 A 3 SER A 40 VAL A 43 -1 N LYS A 42 O THR A 4 SHEET 1 B 4 GLY A 21 TYR A 23 0 SHEET 2 B 4 SER A 80 SER A 85 -1 N VAL A 83 O GLY A 21 SHEET 3 B 4 VAL A 47 TYR A 52 -1 N TYR A 52 O SER A 80 SHEET 4 B 4 GLN A 61 VAL A 64 -1 N VAL A 64 O ALA A 49

LINK CA CA A 90 O TYR A 7 1555 1555 2.05 LINK CA CA A 90 OG SER A 39 1555 1555 1.81 LINK CA CA A 90 O THR A 37 1555 1555 2.12 LINK CA CA A 90 OD1 ASN A 76 1555 1555 2.11 LINK CA CA A 90 O HOH A 166 1555 1555 1.58 LINK CA CA A 145 O ASN A 77 1555 1555 3.37 LINK CA CA A 145 OG SER A 79 1555 1555 2.12 LINK CA CA A 145 O HOH A 93 1555 1555 2.03 LINK CA CA A 145 O GLN A 53 1555 1555 2.41 LINK CA CA A 145 O HOH A 92 1555 1555 1.72 LINK CA CA A 145 O HOH A 99 1555 1555 1.54 LINK CA CA A 145 OD1 ASN A 36 1555 1555 2.22

SITE 1 AC1 5 TYR A 7 THR A 37 SER A 39 ASN A 76 SITE 2 AC1 5 HOH A 166 SITE 1 AC2 7 ASN A 36 GLN A 53 ASN A 77 SER A 79 SITE 2 AC2 7 HOH A 92 HOH A 93 HOH A 99

CRYST1 28.360 37.940 37.260 90.00 105.93 90.00 P 1 21 1 2

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 0.035261 0.000000 0.010064 0.00000

SCALE2 0.000000 0.026357 0.000000 0.00000

SCALE3 0.000000 0.000000 0.027910 0.00000