HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 20-OCT-00 1G2R
TITLE STRUCTURE OF CYTOSOLIC PROTEIN OF UNKNOWN FUNCTION CODED BY GENE FROM
TITLE 2 NUSA/INFB REGION, A YLXR HOMOLOGUE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HYPOTHETICAL CYTOSOLIC PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE;
SOURCE 3 ORGANISM_TAXID: 1313;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS HYPOTHETICAL, NUSA-INFB OPERON, STREPTOCOCCUS PNEUMONIAE, STRUCTURAL
KEYWDS 2 GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR
KEYWDS 3 STRUCTURAL GENOMICS, MCSG, UNKNOWN FUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR J.OSIPIUK,P.GORNICKI,L.MAJ,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL
AUTHOR 2 GENOMICS (MCSG)
REVDAT 6 07-FEB-24 1G2R 1 REMARK SEQADV
REVDAT 5 24-FEB-09 1G2R 1 VERSN
REVDAT 4 12-APR-05 1G2R 1 SOURCE
REVDAT 3 29-MAR-05 1G2R 1 JRNL
REVDAT 2 18-JAN-05 1G2R 1 AUTHOR KEYWDS REMARK
REVDAT 1 29-AUG-01 1G2R 0
JRNL AUTH J.OSIPIUK,P.GORNICKI,L.MAJ,I.DEMENTIEVA,R.LASKOWSKI,
JRNL AUTH 2 A.JOACHIMIAK
JRNL TITL STREPTOCOCCUS PNEUMONIA YLXR AT 1.35 A SHOWS A PUTATIVE NEW
JRNL TITL 2 FOLD.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 1747 2001
JRNL REFN ISSN 0907-4449
JRNL PMID 11679764
JRNL DOI 10.1107/S0907444901014019
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.40
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2
REMARK 3 NUMBER OF REFLECTIONS : 21402
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.156
REMARK 3 R VALUE (WORKING SET) : 0.157
REMARK 3 FREE R VALUE : 0.185
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300
REMARK 3 FREE R VALUE TEST SET COUNT : 1573
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 767
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 15
REMARK 3 SOLVENT ATOMS : 131
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 15.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.14000
REMARK 3 B22 (A**2) : 0.30000
REMARK 3 B33 (A**2) : -0.44000
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 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) : 0.013 ; 0.020
REMARK 3 ANGLE DISTANCE (A) : 0.031 ; 0.040
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.034 ; 0.050
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 1G2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-00.
REMARK 100 THE DEPOSITION ID IS D_1000012161.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-AUG-00
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 19-BM
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332
REMARK 200 MONOCHROMATOR : SI 111
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101345
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5
REMARK 200 DATA REDUNDANCY : 4.800
REMARK 200 R MERGE (I) : 0.06300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37
REMARK 200 COMPLETENESS FOR SHELL (%) : 61.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.90
REMARK 200 R MERGE FOR SHELL (I) : 0.26900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.62
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE, 0.1 M
REMARK 280 TRI-SODIUM CITRATE, 2.0 M AMMONIUM SULFATE, PH 5.6, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 283K
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 14.02500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.84500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.37500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.84500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.02500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.37500
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 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 GLY A -2
REMARK 465 SER A -1
REMARK 465 HIS A 0
REMARK 465 MET A 1
REMARK 465 LYS A 2
REMARK 465 THR A 3
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 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 GLU A 80 OE1 - CD - OE2 ANGL. DEV. = -10.3 DEGREES
REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 ALA A 42 10.50
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 103
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: APC085 RELATED DB: TARGETDB
DBREF 1G2R A 1 97 UNP Q97S59 Q97S59_STRPN 1 97
SEQADV 1G2R GLY A -2 UNP Q97S59 CLONING ARTIFACT
SEQADV 1G2R SER A -1 UNP Q97S59 CLONING ARTIFACT
SEQADV 1G2R HIS A 0 UNP Q97S59 CLONING ARTIFACT
SEQRES 1 A 100 GLY SER HIS MET LYS THR ARG LYS ILE PRO LEU ARG LYS
SEQRES 2 A 100 SER VAL VAL SER ASN GLU VAL ILE ASP LYS ARG ASP LEU
SEQRES 3 A 100 LEU ARG ILE VAL LYS ASN LYS GLU GLY GLN VAL PHE ILE
SEQRES 4 A 100 ASP PRO THR GLY LYS ALA ASN GLY ARG GLY ALA TYR ILE
SEQRES 5 A 100 LYS LEU ASP ASN ALA GLU ALA LEU GLU ALA LYS LYS LYS
SEQRES 6 A 100 LYS VAL PHE ASN ARG SER PHE SER MET GLU VAL GLU GLU
SEQRES 7 A 100 SER PHE TYR ASP GLU LEU ILE ALA TYR VAL ASP HIS LYS
SEQRES 8 A 100 VAL LYS ARG ARG GLU LEU GLY LEU GLU
HET SO4 A 101 5
HET SO4 A 102 5
HET SO4 A 103 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 3(O4 S 2-)
FORMUL 5 HOH *131(H2 O)
HELIX 1 1 ASP A 19 ARG A 21 5 3
HELIX 2 2 ASP A 52 LYS A 63 1 12
HELIX 3 3 LYS A 63 SER A 70 1 8
HELIX 4 4 GLU A 74 LEU A 94 1 21
SHEET 1 A 3 VAL A 34 ASP A 37 0
SHEET 2 A 3 LEU A 23 LYS A 28 -1 O ARG A 25 N ASP A 37
SHEET 3 A 3 ARG A 45 LYS A 50 -1 N ARG A 45 O LYS A 28
SITE 1 AC1 6 LYS A 50 LYS A 61 HOH A 205 HOH A 234
SITE 2 AC1 6 HOH A 262 HOH A 324
SITE 1 AC2 9 ARG A 9 LYS A 10 GLU A 16 LYS A 61
SITE 2 AC2 9 HOH A 208 HOH A 232 HOH A 262 HOH A 289
SITE 3 AC2 9 HOH A 310
SITE 1 AC3 9 ARG A 9 ARG A 25 GLY A 46 TYR A 48
SITE 2 AC3 9 LYS A 60 HOH A 219 HOH A 238 HOH A 239
SITE 3 AC3 9 HOH A 251
CRYST1 28.050 48.750 73.690 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 0.035651 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020513 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013570 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
