HEADER LYASE 09-MAR-11 3R13
TITLE CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE (TM_1559) FROM
TITLE 2 THERMOTOGA MARITIMA AT 1.83 A RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DEOXYRIBOSE-PHOSPHATE ALDOLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: PHOSPHODEOXYRIBOALDOLASE, DERA, DEOXYRIBOALDOLASE;
COMPND 5 EC: 4.1.2.4;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA;
SOURCE 3 ORGANISM_TAXID: 2336;
SOURCE 4 GENE: DEOC, TM1559, TM_1559;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DL41;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MH1
KEYWDS TIM BETA/ALPHA-BARREL, STRUCTURAL GENOMICS, JOINT CENTER FOR
KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG)
REVDAT 4 01-FEB-23 3R13 1 REMARK SEQADV SHEET LINK
REVDAT 3 08-NOV-17 3R13 1 REMARK
REVDAT 2 20-JUL-11 3R13 1 HETATM REMARK
REVDAT 1 30-MAR-11 3R13 0
JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG)
JRNL TITL CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE
JRNL TITL 2 (TM_1559) FROM THERMOTOGA MARITIMA AT 1.83 A RESOLUTION
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.83 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0110
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.68
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 42154
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) : 0.155
REMARK 3 FREE R VALUE : 0.193
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2116
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.83
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2932
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2590
REMARK 3 BIN FREE R VALUE SET COUNT : 164
REMARK 3 BIN FREE R VALUE : 0.2960
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3978
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 48
REMARK 3 SOLVENT ATOMS : 259
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.80000
REMARK 3 B22 (A**2) : -0.38000
REMARK 3 B33 (A**2) : 1.17000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.01000
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): 0.120
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.131
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4312 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2924 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5830 ; 1.432 ; 1.954
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7160 ; 0.899 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 560 ; 5.958 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;32.897 ;23.859
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 768 ;13.512 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.844 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 644 ; 0.091 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4892 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 877 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2689 ; 1.708 ; 3.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1111 ; 0.593 ; 3.000
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4343 ; 2.822 ; 5.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1623 ; 5.239 ; 8.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1483 ; 8.161 ;11.000
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1
REMARK 3
REMARK 3 NCS GROUP NUMBER : 1
REMARK 3 CHAIN NAMES : A B
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A 1 A 205 5
REMARK 3 1 B 1 B 205 5
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 MEDIUM POSITIONAL 1 A (A): 1163 ; 0.080 ; 0.500
REMARK 3 LOOSE POSITIONAL 1 A (A): 1427 ; 0.380 ; 5.000
REMARK 3 MEDIUM THERMAL 1 A (A**2): 1163 ; 0.750 ; 2.000
REMARK 3 LOOSE THERMAL 1 A (A**2): 1427 ; 0.910 ;10.000
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A -9 A 247
REMARK 3 ORIGIN FOR THE GROUP (A): 3.5890 23.1970 54.5460
REMARK 3 T TENSOR
REMARK 3 T11: 0.0390 T22: 0.0420
REMARK 3 T33: 0.0046 T12: -0.0037
REMARK 3 T13: 0.0052 T23: -0.0062
REMARK 3 L TENSOR
REMARK 3 L11: 1.1087 L22: 0.6984
REMARK 3 L33: 0.4405 L12: 0.0296
REMARK 3 L13: 0.1435 L23: 0.0925
REMARK 3 S TENSOR
REMARK 3 S11: 0.0110 S12: 0.0768 S13: -0.0031
REMARK 3 S21: -0.0077 S22: -0.0157 S23: -0.0055
REMARK 3 S31: 0.0776 S32: -0.0114 S33: 0.0047
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B -9 B 248
REMARK 3 ORIGIN FOR THE GROUP (A): 7.0310 43.3440 77.9150
REMARK 3 T TENSOR
REMARK 3 T11: 0.0363 T22: 0.0055
REMARK 3 T33: 0.0485 T12: -0.0003
REMARK 3 T13: -0.0027 T23: -0.0038
REMARK 3 L TENSOR
REMARK 3 L11: 0.7991 L22: 0.4931
REMARK 3 L33: 0.5957 L12: 0.0736
REMARK 3 L13: 0.1150 L23: 0.1299
REMARK 3 S TENSOR
REMARK 3 S11: 0.0089 S12: -0.0528 S13: 0.0172
REMARK 3 S21: 0.0881 S22: -0.0194 S23: -0.0114
REMARK 3 S31: 0.0029 S32: -0.0157 S33: 0.0105
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE
REMARK 3 RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR
REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE
REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO
REMARK 3 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL
REMARK 3 S-MET INCORPORATION. 3. THE ELECTRON DENSITY REVEALS THAT LYSINE
REMARK 3 179 HAS BEEN COVALENTLY MODIFIED. IT WAS MODELED AS AN UNKNOWN
REMARK 3 LIGAND (UNL). 4. ACETATE (ACT) AND GLYCEROL (GOL) MODELED IN THE
REMARK 3 STRUCTURE ARE PRESENT IN CRYO/PROTEIN BUFFERS. 5. ATOM RECORD
REMARK 3 CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD
REMARK 3 CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 6. WATERS WERE
REMARK 3 EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
REMARK 4
REMARK 4 3R13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-11.
REMARK 100 THE DEPOSITION ID IS D_1000064356.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 31-MAR-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL9-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.89194,0.97946,0.97929
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL
REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5, XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42195
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830
REMARK 200 RESOLUTION RANGE LOW (A) : 44.677
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : 0.09400
REMARK 200 R SYM (I) : 0.09400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : 0.55200
REMARK 200 R SYM FOR SHELL (I) : 0.55200
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD, AUTOSHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.21
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 40.0% 1,2-PROPANEDIOL, 0.05M CALCIUM
REMARK 280 ACETATE, 0.1M ACETATE PH 4.5, NANODROP, VAPOR DIFFUSION, SITTING
REMARK 280 DROP, TEMPERATURE 277K
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 26.24050
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4470 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20980 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MSE A -11
REMARK 465 GLY A -10
REMARK 465 GLY A 248
REMARK 465 MSE B -11
REMARK 465 GLY B -10
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 LYS A -7 CG CD CE NZ
REMARK 470 ARG A 5 CZ NH1 NH2
REMARK 470 GLU A 24 CG CD OE1 OE2
REMARK 470 GLU A 79 CD OE1 OE2
REMARK 470 GLU A 204 CG CD OE1 OE2
REMARK 470 LYS B -7 CG CD CE NZ
REMARK 470 GLU B 79 CD OE1 OE2
REMARK 470 GLY B 248 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 GLU B 154 69.11 60.94
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 ACT A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 308
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 283416 RELATED DB: TARGETDB
REMARK 900 RELATED ID: 3R12 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A DEOXYRIBOSE-PHOSPHATE ALDOLASE (TM_1559)
REMARK 900 FROM THERMOTOGA MARITIMA AT 1.75 A RESOLUTION (APO FORM)
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.
DBREF 3R13 A 1 248 UNP Q9X1P5 DEOC_THEMA 1 248
DBREF 3R13 B 1 248 UNP Q9X1P5 DEOC_THEMA 1 248
SEQADV 3R13 MSE A -11 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 GLY A -10 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 SER A -9 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 ASP A -8 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 LYS A -7 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 ILE A -6 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS A -5 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS A -4 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS A -3 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS A -2 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS A -1 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS A 0 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 MSE B -11 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 GLY B -10 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 SER B -9 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 ASP B -8 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 LYS B -7 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 ILE B -6 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS B -5 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS B -4 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS B -3 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS B -2 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS B -1 UNP Q9X1P5 EXPRESSION TAG
SEQADV 3R13 HIS B 0 UNP Q9X1P5 EXPRESSION TAG
SEQRES 1 A 260 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE
SEQRES 2 A 260 ILE GLU TYR ARG ILE GLU GLU ALA VAL ALA LYS TYR ARG
SEQRES 3 A 260 GLU PHE TYR GLU PHE LYS PRO VAL ARG GLU SER ALA GLY
SEQRES 4 A 260 ILE GLU ASP VAL LYS SER ALA ILE GLU HIS THR ASN LEU
SEQRES 5 A 260 LYS PRO PHE ALA THR PRO ASP ASP ILE LYS LYS LEU CYS
SEQRES 6 A 260 LEU GLU ALA ARG GLU ASN ARG PHE HIS GLY VAL CYS VAL
SEQRES 7 A 260 ASN PRO CYS TYR VAL LYS LEU ALA ARG GLU GLU LEU GLU
SEQRES 8 A 260 GLY THR ASP VAL LYS VAL VAL THR VAL VAL GLY PHE PRO
SEQRES 9 A 260 LEU GLY ALA ASN GLU THR ARG THR LYS ALA HIS GLU ALA
SEQRES 10 A 260 ILE PHE ALA VAL GLU SER GLY ALA ASP GLU ILE ASP MSE
SEQRES 11 A 260 VAL ILE ASN VAL GLY MSE LEU LYS ALA LYS GLU TRP GLU
SEQRES 12 A 260 TYR VAL TYR GLU ASP ILE ARG SER VAL VAL GLU SER VAL
SEQRES 13 A 260 LYS GLY LYS VAL VAL LYS VAL ILE ILE GLU THR CYS TYR
SEQRES 14 A 260 LEU ASP THR GLU GLU LYS ILE ALA ALA CYS VAL ILE SER
SEQRES 15 A 260 LYS LEU ALA GLY ALA HIS PHE VAL LYS THR SER THR GLY
SEQRES 16 A 260 PHE GLY THR GLY GLY ALA THR ALA GLU ASP VAL HIS LEU
SEQRES 17 A 260 MSE LYS TRP ILE VAL GLY ASP GLU MSE GLY VAL LYS ALA
SEQRES 18 A 260 SER GLY GLY ILE ARG THR PHE GLU ASP ALA VAL LYS MSE
SEQRES 19 A 260 ILE MSE TYR GLY ALA ASP ARG ILE GLY THR SER SER GLY
SEQRES 20 A 260 VAL LYS ILE VAL GLN GLY GLY GLU GLU ARG TYR GLY GLY
SEQRES 1 B 260 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE
SEQRES 2 B 260 ILE GLU TYR ARG ILE GLU GLU ALA VAL ALA LYS TYR ARG
SEQRES 3 B 260 GLU PHE TYR GLU PHE LYS PRO VAL ARG GLU SER ALA GLY
SEQRES 4 B 260 ILE GLU ASP VAL LYS SER ALA ILE GLU HIS THR ASN LEU
SEQRES 5 B 260 LYS PRO PHE ALA THR PRO ASP ASP ILE LYS LYS LEU CYS
SEQRES 6 B 260 LEU GLU ALA ARG GLU ASN ARG PHE HIS GLY VAL CYS VAL
SEQRES 7 B 260 ASN PRO CYS TYR VAL LYS LEU ALA ARG GLU GLU LEU GLU
SEQRES 8 B 260 GLY THR ASP VAL LYS VAL VAL THR VAL VAL GLY PHE PRO
SEQRES 9 B 260 LEU GLY ALA ASN GLU THR ARG THR LYS ALA HIS GLU ALA
SEQRES 10 B 260 ILE PHE ALA VAL GLU SER GLY ALA ASP GLU ILE ASP MSE
SEQRES 11 B 260 VAL ILE ASN VAL GLY MSE LEU LYS ALA LYS GLU TRP GLU
SEQRES 12 B 260 TYR VAL TYR GLU ASP ILE ARG SER VAL VAL GLU SER VAL
SEQRES 13 B 260 LYS GLY LYS VAL VAL LYS VAL ILE ILE GLU THR CYS TYR
SEQRES 14 B 260 LEU ASP THR GLU GLU LYS ILE ALA ALA CYS VAL ILE SER
SEQRES 15 B 260 LYS LEU ALA GLY ALA HIS PHE VAL LYS THR SER THR GLY
SEQRES 16 B 260 PHE GLY THR GLY GLY ALA THR ALA GLU ASP VAL HIS LEU
SEQRES 17 B 260 MSE LYS TRP ILE VAL GLY ASP GLU MSE GLY VAL LYS ALA
SEQRES 18 B 260 SER GLY GLY ILE ARG THR PHE GLU ASP ALA VAL LYS MSE
SEQRES 19 B 260 ILE MSE TYR GLY ALA ASP ARG ILE GLY THR SER SER GLY
SEQRES 20 B 260 VAL LYS ILE VAL GLN GLY GLY GLU GLU ARG TYR GLY GLY
MODRES 3R13 MSE A 1 MET SELENOMETHIONINE
MODRES 3R13 MSE A 118 MET SELENOMETHIONINE
MODRES 3R13 MSE A 124 MET SELENOMETHIONINE
MODRES 3R13 MSE A 197 MET SELENOMETHIONINE
MODRES 3R13 MSE A 205 MET SELENOMETHIONINE
MODRES 3R13 MSE A 222 MET SELENOMETHIONINE
MODRES 3R13 MSE A 224 MET SELENOMETHIONINE
MODRES 3R13 MSE B 1 MET SELENOMETHIONINE
MODRES 3R13 MSE B 118 MET SELENOMETHIONINE
MODRES 3R13 MSE B 124 MET SELENOMETHIONINE
MODRES 3R13 MSE B 197 MET SELENOMETHIONINE
MODRES 3R13 MSE B 205 MET SELENOMETHIONINE
MODRES 3R13 MSE B 222 MET SELENOMETHIONINE
MODRES 3R13 MSE B 224 MET SELENOMETHIONINE
HET MSE A 1 24
HET MSE A 118 8
HET MSE A 124 8
HET MSE A 197 8
HET MSE A 205 16
HET MSE A 222 8
HET MSE A 224 8
HET MSE B 1 16
HET MSE B 118 8
HET MSE B 124 8
HET MSE B 197 8
HET MSE B 205 8
HET MSE B 222 8
HET MSE B 224 8
HET UNL A 300 6
HET ACT A 301 4
HET ACT A 302 4
HET ACT A 306 4
HET GOL A 307 6
HET ACT B 303 4
HET UNL B 300 6
HET ACT B 304 4
HET ACT B 305 4
HET GOL B 308 6
HETNAM MSE SELENOMETHIONINE
HETNAM UNL UNKNOWN LIGAND
HETNAM ACT ACETATE ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 MSE 14(C5 H11 N O2 SE)
FORMUL 4 ACT 6(C2 H3 O2 1-)
FORMUL 7 GOL 2(C3 H8 O3)
FORMUL 13 HOH *259(H2 O)
HELIX 1 1 SER A -9 TYR A 17 1 27
HELIX 2 2 GLY A 27 ALA A 34 1 8
HELIX 3 3 THR A 45 ARG A 60 1 16
HELIX 4 4 TYR A 70 LEU A 78 1 9
HELIX 5 5 GLU A 97 SER A 111 1 15
HELIX 6 6 ASN A 121 ALA A 127 1 7
HELIX 7 7 GLU A 129 VAL A 144 1 16
HELIX 8 8 GLU A 154 LEU A 158 5 5
HELIX 9 9 ASP A 159 ALA A 173 1 15
HELIX 10 10 THR A 190 GLY A 202 1 13
HELIX 11 11 THR A 215 TYR A 225 1 11
HELIX 12 12 SER A 234 GLY A 247 1 14
HELIX 13 13 SER B -9 TYR B 17 1 27
HELIX 14 14 GLY B 27 ALA B 34 1 8
HELIX 15 15 THR B 45 ARG B 60 1 16
HELIX 16 16 TYR B 70 GLU B 79 1 10
HELIX 17 17 GLU B 97 SER B 111 1 15
HELIX 18 18 ASN B 121 ALA B 127 1 7
HELIX 19 19 GLU B 129 VAL B 144 1 16
HELIX 20 20 GLU B 154 LEU B 158 5 5
HELIX 21 21 ASP B 159 ALA B 173 1 15
HELIX 22 22 THR B 190 GLY B 202 1 13
HELIX 23 23 THR B 215 TYR B 225 1 11
HELIX 24 24 SER B 234 GLY B 247 1 14
SHEET 1 A 8 ILE A 35 ASN A 39 0
SHEET 2 A 8 GLY A 63 VAL A 66 1 O CYS A 65 N ASN A 39
SHEET 3 A 8 LYS A 84 VAL A 89 1 O VAL A 86 N VAL A 64
SHEET 4 A 8 GLU A 115 VAL A 119 1 O ASP A 117 N THR A 87
SHEET 5 A 8 VAL A 148 ILE A 152 1 O ILE A 152 N MSE A 118
SHEET 6 A 8 GLY A 206 SER A 210 1 O LYS A 208 N VAL A 178
SHEET 7 A 8 ARG A 229 THR A 232 1 O GLY A 231 N ALA A 209
SHEET 8 A 8 ILE A 35 ASN A 39 1 N THR A 38 O THR A 232
SHEET 1 B 8 ILE B 35 ASN B 39 0
SHEET 2 B 8 GLY B 63 VAL B 66 1 O GLY B 63 N HIS B 37
SHEET 3 B 8 LYS B 84 VAL B 89 1 O LYS B 84 N VAL B 64
SHEET 4 B 8 GLU B 115 VAL B 119 1 O ASP B 117 N THR B 87
SHEET 5 B 8 VAL B 148 ILE B 152 1 O ILE B 152 N MSE B 118
SHEET 6 B 8 GLY B 206 SER B 210 1 O LYS B 208 N VAL B 178
SHEET 7 B 8 ARG B 229 THR B 232 1 O GLY B 231 N ALA B 209
SHEET 8 B 8 ILE B 35 ASN B 39 1 N GLU B 36 O ILE B 230
LINK C HIS A 0 N AMSE A 1 1555 1555 1.33
LINK C HIS A 0 N BMSE A 1 1555 1555 1.34
LINK C HIS A 0 N CMSE A 1 1555 1555 1.34
LINK C AMSE A 1 N ILE A 2 1555 1555 1.34
LINK C BMSE A 1 N ILE A 2 1555 1555 1.33
LINK C CMSE A 1 N ILE A 2 1555 1555 1.33
LINK C ASP A 117 N MSE A 118 1555 1555 1.34
LINK C MSE A 118 N VAL A 119 1555 1555 1.35
LINK C GLY A 123 N MSE A 124 1555 1555 1.32
LINK C MSE A 124 N LEU A 125 1555 1555 1.34
LINK NZ LYS A 179 C1' UNL A 300 1555 1555 1.45
LINK C LEU A 196 N MSE A 197 1555 1555 1.33
LINK C MSE A 197 N LYS A 198 1555 1555 1.32
LINK C GLU A 204 N AMSE A 205 1555 1555 1.32
LINK C GLU A 204 N BMSE A 205 1555 1555 1.34
LINK C AMSE A 205 N GLY A 206 1555 1555 1.32
LINK C BMSE A 205 N GLY A 206 1555 1555 1.33
LINK C LYS A 221 N MSE A 222 1555 1555 1.32
LINK C MSE A 222 N ILE A 223 1555 1555 1.33
LINK C ILE A 223 N MSE A 224 1555 1555 1.33
LINK C MSE A 224 N TYR A 225 1555 1555 1.33
LINK C AHIS B 0 N AMSE B 1 1555 1555 1.33
LINK C BHIS B 0 N BMSE B 1 1555 1555 1.33
LINK C AMSE B 1 N ILE B 2 1555 1555 1.33
LINK C BMSE B 1 N ILE B 2 1555 1555 1.34
LINK C ASP B 117 N MSE B 118 1555 1555 1.34
LINK C MSE B 118 N VAL B 119 1555 1555 1.32
LINK C GLY B 123 N MSE B 124 1555 1555 1.33
LINK C MSE B 124 N LEU B 125 1555 1555 1.32
LINK NZ LYS B 179 C1' UNL B 300 1555 1555 1.47
LINK C LEU B 196 N MSE B 197 1555 1555 1.33
LINK C MSE B 197 N LYS B 198 1555 1555 1.34
LINK C GLU B 204 N MSE B 205 1555 1555 1.32
LINK C MSE B 205 N GLY B 206 1555 1555 1.33
LINK C LYS B 221 N MSE B 222 1555 1555 1.34
LINK C MSE B 222 N ILE B 223 1555 1555 1.33
LINK C ILE B 223 N MSE B 224 1555 1555 1.32
LINK C MSE B 224 N TYR B 225 1555 1555 1.33
CISPEP 1 PHE A 91 PRO A 92 0 2.22
CISPEP 2 PHE B 91 PRO B 92 0 1.85
SITE 1 AC1 3 TYR A 13 ARG A 14 TYR A 17
SITE 1 AC2 1 TYR A 157
SITE 1 AC3 1 ILE A 200
SITE 1 AC4 8 GLY A 212 ILE A 213 ARG A 214 THR A 232
SITE 2 AC4 8 SER A 233 SER A 234 HOH A 320 HOH A 400
SITE 1 AC5 1 CYS B 69
SITE 1 AC6 2 ARG B 14 GLU B 161
SITE 1 AC7 2 GLY B 187 GLY B 188
SITE 1 AC8 7 ILE B 213 ARG B 214 THR B 232 SER B 233
SITE 2 AC8 7 SER B 234 HOH B 331 HOH B 420
CRYST1 53.904 52.481 85.462 90.00 95.59 90.00 P 1 21 1 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 0.018551 0.000000 0.001816 0.00000
SCALE2 0.000000 0.019055 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011757 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
