HEADER HYDROLASE 29-JUL-08 3DZI
TITLE CRYSTAL STRUCTURE OF HUMAN CD38 EXTRACELLULAR DOMAIN, RIBOSE-5'-
TITLE 2 PHOSPHATE INTERMEDIATE/GTP COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ADP-RIBOSYL CYCLASE 1;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: ENZYMATIC DOMAIN: UNP RESIDUES 45-300;
COMPND 5 SYNONYM: CYCLIC ADP-RIBOSE HYDROLASE 1, CADPR HYDROLASE 1, T10, CD38
COMPND 6 ANTIGEN;
COMPND 7 EC: 3.2.2.5;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_TAXID: 9606;
SOURCE 4 GENE: CD38;
SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: X-33 (INVITROGEN);
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPICZ(ALPHA)A
KEYWDS NONCOVALENT INTERMEDIATE, GTP COMPLEX, R5P-GTP ADDUCT, BETA SHEETS,
KEYWDS 2 ALPHA BUNDLE, ALTERNATIVE SPLICING, DIABETES MELLITUS, GLYCOPROTEIN,
KEYWDS 3 HYDROLASE, MEMBRANE, NAD, POLYMORPHISM, RECEPTOR, SIGNAL-ANCHOR,
KEYWDS 4 TRANSMEMBRANE
EXPDTA X-RAY DIFFRACTION
AUTHOR Q.LIU,I.A.KRIKSUNOV,H.JIANG,R.GRAEFF,H.LIN,H.C.LEE,Q.HAO
REVDAT 5 30-OCT-24 3DZI 1 REMARK
REVDAT 4 30-AUG-23 3DZI 1 REMARK
REVDAT 3 20-OCT-21 3DZI 1 REMARK SEQADV
REVDAT 2 24-FEB-09 3DZI 1 VERSN
REVDAT 1 04-NOV-08 3DZI 0
JRNL AUTH Q.LIU,I.A.KRIKSUNOV,H.JIANG,R.GRAEFF,H.LIN,H.C.LEE,Q.HAO
JRNL TITL COVALENT AND NONCOVALENT INTERMEDIATES OF AN NAD UTILIZING
JRNL TITL 2 ENZYME, HUMAN CD38.
JRNL REF CHEM.BIOL. V. 15 1068 2008
JRNL REFN ISSN 1074-5521
JRNL PMID 18940667
JRNL DOI 10.1016/J.CHEMBIOL.2008.08.007
REMARK 2
REMARK 2 RESOLUTION. 1.73 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.3.0021
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8
REMARK 3 NUMBER OF REFLECTIONS : 50238
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) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.177
REMARK 3 FREE R VALUE : 0.211
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2691
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) : 1.73
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3151
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.41
REMARK 3 BIN R VALUE (WORKING SET) : 0.2380
REMARK 3 BIN FREE R VALUE SET COUNT : 176
REMARK 3 BIN FREE R VALUE : 0.2760
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4100
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 90
REMARK 3 SOLVENT ATOMS : 344
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.48
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.23000
REMARK 3 B22 (A**2) : 0.66000
REMARK 3 B33 (A**2) : 1.32000
REMARK 3 B12 (A**2) : 0.42000
REMARK 3 B13 (A**2) : 0.44000
REMARK 3 B23 (A**2) : 1.17000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.119
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.060
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4308 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5862 ; 1.566 ; 1.960
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 502 ; 6.012 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;36.723 ;24.038
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 742 ;16.060 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.108 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 626 ; 0.105 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3226 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2098 ; 0.232 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2927 ; 0.314 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 336 ; 0.154 ; 0.200
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): 76 ; 0.223 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.157 ; 0.200
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): 2575 ; 0.959 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4114 ; 1.530 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1992 ; 2.535 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1748 ; 4.046 ; 4.500
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 : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3DZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-08.
REMARK 100 THE DEPOSITION ID IS D_1000048684.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-MAY-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CHESS
REMARK 200 BEAMLINE : A1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53519
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.04200
REMARK 200 R SYM (I) : 0.04200
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79
REMARK 200 COMPLETENESS FOR SHELL (%) : 82.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.45800
REMARK 200 R SYM FOR SHELL (I) : 0.45800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 1YH3
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.74
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.0, 15% PEG 4000, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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 LYS A 39
REMARK 465 ARG A 40
REMARK 465 GLU A 41
REMARK 465 ALA A 42
REMARK 465 GLU A 43
REMARK 465 ALA A 44
REMARK 465 THR A 297
REMARK 465 SER A 298
REMARK 465 GLU A 299
REMARK 465 ILE A 300
REMARK 465 LYS B 39
REMARK 465 ARG B 40
REMARK 465 GLU B 41
REMARK 465 ALA B 42
REMARK 465 GLU B 43
REMARK 465 ALA B 44
REMARK 465 THR B 297
REMARK 465 SER B 298
REMARK 465 GLU B 299
REMARK 465 ILE B 300
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 O4' N B 301 O6 GTP B 302 2.14
REMARK 500 C1' N B 301 O6 GTP B 302 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A 72 CB GLU A 72 CG 0.116
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 ARG A 127 -47.02 73.81
REMARK 500 GLN A 139 22.08 -153.32
REMARK 500 ASP A 179 -68.95 -108.28
REMARK 500 ASP A 202 -122.85 62.11
REMARK 500 VAL A 225 -59.24 -120.83
REMARK 500 GLU A 248 -135.43 66.63
REMARK 500 GLU A 292 -2.10 60.36
REMARK 500 SER A 294 -110.14 -105.63
REMARK 500 SER A 295 42.44 -97.17
REMARK 500 SER B 95 -9.93 77.04
REMARK 500 ILE B 128 51.70 -149.28
REMARK 500 ASP B 179 -74.89 -109.29
REMARK 500 ASP B 202 -117.19 57.88
REMARK 500 GLU B 248 -162.59 54.28
REMARK 500 ASP B 249 -176.33 -69.04
REMARK 500 GLU B 292 48.47 -103.32
REMARK 500 SER B 294 73.13 44.77
REMARK 500 SER B 295 100.52 -29.88
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 AUTHORS STATE THAT THE LIGAND [N] IN THIS ENTRY IS A
REMARK 600 REACTION INTERMEDIATE, WITH THE (C1') ATOM HAVING SP2
REMARK 600 HYBRIDIZATION (C1'H), NOT THE SP3 HYBRIDIZATION (C1'H2).
REMARK 600 AUTHORS ALSO STATE THAT THE LIGAND RGT THAT IS PRESENT
REMARK 600 IN THIS ENTRY IS ALSO AN UNSTABLE INTERMEDIATE AND
REMARK 600 THEREFORE THE DISTORTED LINKAGE BETWEEN RIBOSE-PHOSPHATE
REMARK 600 AND GTP MOIETIES REFLECTS THE CHEMISTRY OF THE REACTION.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RGT A 301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3DZF RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, ARA-2-DEOXY-2-FLUORO-RIBOSE-5'-
REMARK 900 PHOSPHATE COMPLEX
REMARK 900 RELATED ID: 3DZG RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, ARA-2-DEOXY-2-FLUORO-RIBOSE-5'-
REMARK 900 PHOSPHATE/NICOTINAMIDE COMPLEX
REMARK 900 RELATED ID: 3DZH RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, GTP COMPLEX
REMARK 900 RELATED ID: 3DZJ RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN E226Q MUTANT, NMN COMPLEX
REMARK 900 RELATED ID: 3DZK RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, NMN COMPLEX
DBREF 3DZI A 45 300 UNP P28907 CD38_HUMAN 45 300
DBREF 3DZI B 45 300 UNP P28907 CD38_HUMAN 45 300
SEQADV 3DZI LYS A 39 UNP P28907 EXPRESSION TAG
SEQADV 3DZI ARG A 40 UNP P28907 EXPRESSION TAG
SEQADV 3DZI GLU A 41 UNP P28907 EXPRESSION TAG
SEQADV 3DZI ALA A 42 UNP P28907 EXPRESSION TAG
SEQADV 3DZI GLU A 43 UNP P28907 EXPRESSION TAG
SEQADV 3DZI ALA A 44 UNP P28907 EXPRESSION TAG
SEQADV 3DZI THR A 49 UNP P28907 GLN 49 ENGINEERED MUTATION
SEQADV 3DZI ASP A 100 UNP P28907 ASN 100 ENGINEERED MUTATION
SEQADV 3DZI ASP A 164 UNP P28907 ASN 164 ENGINEERED MUTATION
SEQADV 3DZI ASP A 209 UNP P28907 ASN 209 ENGINEERED MUTATION
SEQADV 3DZI ASP A 219 UNP P28907 ASN 219 ENGINEERED MUTATION
SEQADV 3DZI LYS B 39 UNP P28907 EXPRESSION TAG
SEQADV 3DZI ARG B 40 UNP P28907 EXPRESSION TAG
SEQADV 3DZI GLU B 41 UNP P28907 EXPRESSION TAG
SEQADV 3DZI ALA B 42 UNP P28907 EXPRESSION TAG
SEQADV 3DZI GLU B 43 UNP P28907 EXPRESSION TAG
SEQADV 3DZI ALA B 44 UNP P28907 EXPRESSION TAG
SEQADV 3DZI THR B 49 UNP P28907 GLN 49 ENGINEERED MUTATION
SEQADV 3DZI ASP B 100 UNP P28907 ASN 100 ENGINEERED MUTATION
SEQADV 3DZI ASP B 164 UNP P28907 ASN 164 ENGINEERED MUTATION
SEQADV 3DZI ASP B 209 UNP P28907 ASN 209 ENGINEERED MUTATION
SEQADV 3DZI ASP B 219 UNP P28907 ASN 219 ENGINEERED MUTATION
SEQRES 1 A 262 LYS ARG GLU ALA GLU ALA ARG TRP ARG GLN THR TRP SER
SEQRES 2 A 262 GLY PRO GLY THR THR LYS ARG PHE PRO GLU THR VAL LEU
SEQRES 3 A 262 ALA ARG CYS VAL LYS TYR THR GLU ILE HIS PRO GLU MET
SEQRES 4 A 262 ARG HIS VAL ASP CYS GLN SER VAL TRP ASP ALA PHE LYS
SEQRES 5 A 262 GLY ALA PHE ILE SER LYS HIS PRO CYS ASP ILE THR GLU
SEQRES 6 A 262 GLU ASP TYR GLN PRO LEU MET LYS LEU GLY THR GLN THR
SEQRES 7 A 262 VAL PRO CYS ASN LYS ILE LEU LEU TRP SER ARG ILE LYS
SEQRES 8 A 262 ASP LEU ALA HIS GLN PHE THR GLN VAL GLN ARG ASP MET
SEQRES 9 A 262 PHE THR LEU GLU ASP THR LEU LEU GLY TYR LEU ALA ASP
SEQRES 10 A 262 ASP LEU THR TRP CYS GLY GLU PHE ASP THR SER LYS ILE
SEQRES 11 A 262 ASN TYR GLN SER CYS PRO ASP TRP ARG LYS ASP CYS SER
SEQRES 12 A 262 ASN ASN PRO VAL SER VAL PHE TRP LYS THR VAL SER ARG
SEQRES 13 A 262 ARG PHE ALA GLU ALA ALA CYS ASP VAL VAL HIS VAL MET
SEQRES 14 A 262 LEU ASP GLY SER ARG SER LYS ILE PHE ASP LYS ASP SER
SEQRES 15 A 262 THR PHE GLY SER VAL GLU VAL HIS ASN LEU GLN PRO GLU
SEQRES 16 A 262 LYS VAL GLN THR LEU GLU ALA TRP VAL ILE HIS GLY GLY
SEQRES 17 A 262 ARG GLU ASP SER ARG ASP LEU CYS GLN ASP PRO THR ILE
SEQRES 18 A 262 LYS GLU LEU GLU SER ILE ILE SER LYS ARG ASN ILE GLN
SEQRES 19 A 262 PHE SER CYS LYS ASN ILE TYR ARG PRO ASP LYS PHE LEU
SEQRES 20 A 262 GLN CYS VAL LYS ASN PRO GLU ASP SER SER CYS THR SER
SEQRES 21 A 262 GLU ILE
SEQRES 1 B 262 LYS ARG GLU ALA GLU ALA ARG TRP ARG GLN THR TRP SER
SEQRES 2 B 262 GLY PRO GLY THR THR LYS ARG PHE PRO GLU THR VAL LEU
SEQRES 3 B 262 ALA ARG CYS VAL LYS TYR THR GLU ILE HIS PRO GLU MET
SEQRES 4 B 262 ARG HIS VAL ASP CYS GLN SER VAL TRP ASP ALA PHE LYS
SEQRES 5 B 262 GLY ALA PHE ILE SER LYS HIS PRO CYS ASP ILE THR GLU
SEQRES 6 B 262 GLU ASP TYR GLN PRO LEU MET LYS LEU GLY THR GLN THR
SEQRES 7 B 262 VAL PRO CYS ASN LYS ILE LEU LEU TRP SER ARG ILE LYS
SEQRES 8 B 262 ASP LEU ALA HIS GLN PHE THR GLN VAL GLN ARG ASP MET
SEQRES 9 B 262 PHE THR LEU GLU ASP THR LEU LEU GLY TYR LEU ALA ASP
SEQRES 10 B 262 ASP LEU THR TRP CYS GLY GLU PHE ASP THR SER LYS ILE
SEQRES 11 B 262 ASN TYR GLN SER CYS PRO ASP TRP ARG LYS ASP CYS SER
SEQRES 12 B 262 ASN ASN PRO VAL SER VAL PHE TRP LYS THR VAL SER ARG
SEQRES 13 B 262 ARG PHE ALA GLU ALA ALA CYS ASP VAL VAL HIS VAL MET
SEQRES 14 B 262 LEU ASP GLY SER ARG SER LYS ILE PHE ASP LYS ASP SER
SEQRES 15 B 262 THR PHE GLY SER VAL GLU VAL HIS ASN LEU GLN PRO GLU
SEQRES 16 B 262 LYS VAL GLN THR LEU GLU ALA TRP VAL ILE HIS GLY GLY
SEQRES 17 B 262 ARG GLU ASP SER ARG ASP LEU CYS GLN ASP PRO THR ILE
SEQRES 18 B 262 LYS GLU LEU GLU SER ILE ILE SER LYS ARG ASN ILE GLN
SEQRES 19 B 262 PHE SER CYS LYS ASN ILE TYR ARG PRO ASP LYS PHE LEU
SEQRES 20 B 262 GLN CYS VAL LYS ASN PRO GLU ASP SER SER CYS THR SER
SEQRES 21 B 262 GLU ILE
HET RGT A 301 45
HET GTP B 302 32
HETNAM RGT 2-AMINO-9-{5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 RGT PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-RIBOFURANOSYL}-9H-
HETNAM 3 RGT PURIN-6-YL 5-O-PHOSPHONO-BETA-D-RIBOFURANOSIDE
HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE
HETSYN RGT (RIBOSE-5'-PHOSPHATE)-(GUANOSINE-5'-TRIPHOSPHATE)
FORMUL 3 RGT C15 H25 N5 O21 P4
FORMUL 5 GTP C10 H16 N5 O14 P3
FORMUL 6 HOH *344(H2 O)
HELIX 1 1 ARG A 58 HIS A 74 1 17
HELIX 2 2 PRO A 75 ARG A 78 5 4
HELIX 3 3 ASP A 81 ILE A 94 1 14
HELIX 4 4 THR A 102 ASP A 105 5 4
HELIX 5 5 TYR A 106 GLY A 113 1 8
HELIX 6 6 ILE A 128 VAL A 138 1 11
HELIX 7 7 THR A 144 ASP A 147 5 4
HELIX 8 8 THR A 148 ASP A 155 1 8
HELIX 9 9 ASN A 183 ALA A 200 1 18
HELIX 10 10 SER A 220 VAL A 225 1 6
HELIX 11 11 VAL A 225 LEU A 230 1 6
HELIX 12 12 ASP A 252 GLN A 255 5 4
HELIX 13 13 ASP A 256 ARG A 269 1 14
HELIX 14 14 ARG A 280 ASN A 290 1 11
HELIX 15 15 ARG B 58 HIS B 74 1 17
HELIX 16 16 PRO B 75 ARG B 78 5 4
HELIX 17 17 ASP B 81 ILE B 94 1 14
HELIX 18 18 THR B 102 ASP B 105 5 4
HELIX 19 19 TYR B 106 GLY B 113 1 8
HELIX 20 20 ILE B 128 GLN B 139 1 12
HELIX 21 21 THR B 144 ASP B 147 5 4
HELIX 22 22 THR B 148 ASP B 155 1 8
HELIX 23 23 ASN B 183 ALA B 200 1 18
HELIX 24 24 SER B 220 VAL B 225 1 6
HELIX 25 25 GLU B 226 LEU B 230 5 5
HELIX 26 26 ASP B 252 GLN B 255 5 4
HELIX 27 27 ASP B 256 ARG B 269 1 14
HELIX 28 28 ARG B 280 ASN B 290 1 11
SHEET 1 A 2 GLY A 52 PRO A 53 0
SHEET 2 A 2 SER A 172 CYS A 173 -1 O CYS A 173 N GLY A 52
SHEET 1 B 4 LEU A 123 SER A 126 0
SHEET 2 B 4 ASP A 202 ASP A 209 1 O HIS A 205 N LEU A 124
SHEET 3 B 4 VAL A 235 ILE A 243 1 O TRP A 241 N VAL A 206
SHEET 4 B 4 GLN A 272 ILE A 278 1 O LYS A 276 N VAL A 242
SHEET 1 C 2 GLY B 52 PRO B 53 0
SHEET 2 C 2 SER B 172 CYS B 173 -1 O CYS B 173 N GLY B 52
SHEET 1 D 4 LEU B 123 SER B 126 0
SHEET 2 D 4 ASP B 202 ASP B 209 1 O HIS B 205 N LEU B 124
SHEET 3 D 4 VAL B 235 ILE B 243 1 O TRP B 241 N VAL B 206
SHEET 4 D 4 GLN B 272 ILE B 278 1 O SER B 274 N ALA B 240
SSBOND 1 CYS A 67 CYS A 82 1555 1555 2.08
SSBOND 2 CYS A 99 CYS A 180 1555 1555 2.08
SSBOND 3 CYS A 119 CYS A 201 1555 1555 2.06
SSBOND 4 CYS A 160 CYS A 173 1555 1555 2.06
SSBOND 5 CYS A 254 CYS A 275 1555 1555 2.13
SSBOND 6 CYS A 287 CYS A 296 1555 1555 2.03
SSBOND 7 CYS B 67 CYS B 82 1555 1555 2.10
SSBOND 8 CYS B 99 CYS B 180 1555 1555 2.09
SSBOND 9 CYS B 119 CYS B 201 1555 1555 2.05
SSBOND 10 CYS B 160 CYS B 173 1555 1555 2.18
SSBOND 11 CYS B 254 CYS B 275 1555 1555 2.07
SSBOND 12 CYS B 287 CYS B 296 1555 1555 2.04
SITE 1 AC1 11 ARG B 127 GLU B 146 ASP B 155 VAL B 185
SITE 2 AC1 11 TRP B 189 SER B 193 THR B 221 N B 301
SITE 3 AC1 11 HOH B 458 HOH B 540 HOH B 579
SITE 1 AC2 22 LEU A 124 TRP A 125 SER A 126 ARG A 127
SITE 2 AC2 22 LYS A 129 LEU A 145 GLU A 146 ASP A 155
SITE 3 AC2 22 ASP A 175 TRP A 176 ARG A 177 VAL A 185
SITE 4 AC2 22 TRP A 189 SER A 193 SER A 220 THR A 221
SITE 5 AC2 22 PHE A 222 GLU A 226 HOH A 303 HOH A 340
SITE 6 AC2 22 HOH A 386 HOH A 426
CRYST1 41.669 52.747 65.133 106.09 91.92 95.27 P 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 0.023999 0.002214 0.001488 0.00000
SCALE2 0.000000 0.019039 0.005587 0.00000
SCALE3 0.000000 0.000000 0.016010 0.00000